Prohibits: (1) the obligation of a portion of such DHS appropriations until the Secretary of Homeland Security submits to the Appropriations Committee of the House of Representatives an immigration enforcement strategy to reduce the number of undocumented aliens; (2) the use of funds in this Act in contravention of the Buy American Act; (3) the obligation of funds for deployment or implementation, on other than a test basis, of the Secure Flight Program until the Secretary has certified, and the Government Accountability Office reports, that specified requirements have been met; and (4) the use of funds in this Act to amend the oath of allegiance required for naturalization or to maintain the U.S. Secret Service as anything other than a distinct entity within DHS.

Requires a reduction in funding for the Transportation Security Administration's Office of Transportation Security Support for every day that an existing requirement to triple the percentage of cargo inspected on passenger aircraft is not implemented.

Directs the Secretary to: (1) develop screening standards and protocols to more thoroughly screen air cargo on passenger and cargo aircraft; and (2) implement a security plan to permit general aviation aircraft to land and take off at Ronald Reagan Washington National Airport.

Prohibits the use of appropriated funds to process petitions for H-1B (specialty occupations) nonimmigrant visas until a specified number of additional aliens with master's or higher degrees are provided such status.

Reserves a portion of appropriated amounts throughout this Act pending submission of required reports.

Department of Homeland Security Appropriations Act, 2006 - Title I: Departmental Management and Operations - Makes appropriations for the Department of Homeland Security (DHS) for FY 2006 for: (1) the Office of the Secretary of Homeland Security and executive management; (2) the Office of the Under Secretary for Management ; (3) the Office of the Chief Financial Officer; (4) the Office of the Chief Information Officer, including for development and acquisition of information technology equipment, software, services, and related activities and for the costs of conversion to narrowband communications; and (5) the Office of Inspector General. Prohibits obligation of a portion of such funds until the Secretary of Homeland Security (Secretary) submits to the Appropriations Committee of the House of Representatives: (1) a strategy to reduce the number of undocumented aliens by 10 percent per year; and (2) all reports required under this Act.

Title II: Security, Enforcement, and Investigations - Makes appropriations for: (1) the Office of the Under Secretary for Border and Transportation Security, including for expenses of the U.S. Visitor and Immigrant Status Indicator Technology project (US-VISIT), and the development and deployment of the Free and Secure Trade (FAST), NEXUS, and Secure Electronic Network for Traveler's Rapid Inspection (SENTRI) systems; (2) Customs and Border Protection (CBP), including for enforcement of laws relating to border security, immigration, customs, and agricultural inspections and regulatory activities related to plant and animal imports and for customs and border protection automated systems; (3) Immigration and Customs Enforcement (ICE), including for Federal Air Marshals, the Federal Protective Service, and immigration and customs enforcement automated systems; (4) the Transportation Security Administration (TSA); (5) the Coast Guard; and (6) the Secret Service. Prohibits obligation of a portion of CBP and ICE funds until the Secretary submits specified reports to the House Appropriations Committee.

Title III: Preparedness and Recovery - Makes appropriations for: (1) the Office of State and Local Government Coordination and Preparedness, including for grants to State and local governments for terrorism prevention activities (sets forth allocations for formula-based grants, law enforcement terrorism prevention grants, discretionary grants for use in high-threat, high density urban areas and for port security, trucking industry security, and transit security, and buffer zone protection grants), firefighter assistance grants, and emergency management performance grants; (2) reimbursement of Federal agencies for the costs of providing support to counter, investigate, or respond to unexpected threats or acts of terrorism; (3) emergency preparedness and response, including for the Office of the Under Secretary for Emergency Preparedness and Response, the Emergency Preparedness and Response Directorate, countering potential biological, disease, and chemical threats to civilian populations, disaster relief, the disaster assistance direct loan program, the Flood Map Modernization Fund, the National Flood Insurance Fund, the National Flood Mitigation Fund, the National Pre-Disaster Mitigation Fund, and an emergency food and shelter program. Limits the aggregate charges assessed during FY 2006 for the Radiological Emergency Preparedness Program.

Title IV: Research and Development, Training, Assessments, and Services - Makes appropriations for: (1) Citizenship and Immigration Services; (2) the Federal Law Enforcement Training Center; (3) information analysis and infrastructure protection, including for the immediate Office of the Under Secretary for Information Analysis and Infrastructure Protection and the management and administration of programs and activities; and (4) the immediate Office of the Under Secretary for Science and Technology, management and administration of programs and activities, and science and technology research, including for locating an alternative site for the National Bio and Agrodefense Laboratory and toward implementing a program to encourage technological innovation in facilitating DHS's mission.

Title V: General Provisions - (Sec. 505) Deems funds made available by this Act for intelligence activities to be specifically authorized by Congress during FY 2006 until the enactment of an Act authorizing intelligence activities for FY 2006.

(Sec. 506) Directs the Federal Law Enforcement Training Center to establish an accrediting body to establish standards for measuring and assessing the quality and effectiveness of Federal law enforcement training programs, facilities, and instructors.

(Sec. 511) Prohibits the use of funds in this Act in contravention of applicable provisions of the Buy America Act.

(Sec. 512) Reduces funding for the TSA's Office of Transportation Security Support by $100,000 per day for every day after enactment of this Act that an existing requirement to triple the percentage of cargo inspected on passenger aircraft is not implemented.

(Sec. 513) Directs the Commandant of the Coast Guard to provide to Congress each year, at the time that the President's budget is submitted, a list of approved but unfunded Coast Guard priorities in the same manner and with the same contents as the unfunded priorities lists submitted by the chiefs of other Armed Services.

(Sec. 515) Directs that TSA's acquisition management system apply to the acquisition of services, as well as equipment, supplies, and materials.

(Sec. 516) Transfers the authority of the Office of Personnel Management (OPM) to conduct personnel security and suitability background investigations of applicants for, or appointees in, DHS positions to DHS.

(Sec. 518) Prohibits the obligation of funds for deployment or implementation of the Secure Flight program or other follow on or successor passenger prescreening program, on other than a test basis, until the Secretary has certified and the Government Accountability Office has reported that specified requirements have been met.

(Sec. 519) Prohibits the use of funds made available in this Act to amend the oath of allegiance required for naturalization under the Immigration and Nationality Act.

(Sec. 520) Prohibits the use of funds appropriated by this Act to process or approve a competition under Office of Management and Budget Circular A-76 for services provided as of June 1, 2004, by employees of DHS's Bureau of Citizenship and Immigration Services who are known as Immigration Information Officers, Contact Representatives, or Investigative Assistants.

(Sec. 521) Prohibits the use of funds to maintain the U.S. Secret Service as anything other than a distinct entity within DHS.

(Sec. 522) Requires the Secretary to develop screening standards and protocols to more thoroughly screen all types of air cargo on passenger and cargo aircraft by March 1, 2006. Withholds specified funds from obligation until such new standards and protocols are implemented.

(Sec. 523) Directs TSA to use existing checked baggage explosive detection equipment and screeners to screen cargo carried on passenger aircraft to the greatest extent practicable at each airport.

(Sec. 524) Directs the Secretary to implement a security plan to permit general aviation aircraft to land and take off at Ronald Reagan Washington National Airport within 90 days after enactment of this Act.

(Sec. 527) Requires the Secretary to use the Transportation Security Clearinghouse as the central identity management system for the deployment and operation of the registered traveler program, the transportation worker identification credential program, and other applicable programs.

(Sec. 528) Prohibits the use of funds made available under this Act by any person other than the DHS privacy officer to alter, direct changes to, delay, or prohibit the transmission to Congress of privacy-related reports required by the Homeland Security Act of 2002.

(Sec. 529) Prohibits the use of funds made available in this or previous appropriations Acts for the payment of salaries of employees serving as a contracting officer's technical representative (COTR) who has not received COTR training.

(Sec. 530) Requires certain recovered or deobligated transportation security funds appropriated or transferred in prior fiscal years to be available only for procurement and installation of explosive detection systems.

(Sec. 531) Rescinds $7 million from unobligated balances in the Department of Homeland Security Working Capital Fund.

(Sec. 533) Prohibits the use of appropriated funds to process petitions for H-1B (specialty occupations) nonimmigrant status until a specified number of additional aliens with master's or higher degrees are provided such status.

(Sec. 534) Limits the use of funds provided in this Act for the payment of salaries to TSA employees with authority to designate documents as Sensitive Security Information (SSI). Makes unavailable $10 million of funds for the DHS-wide Office of Security until the Secretary submits to the House Appropriations Committee specified SSI-related information, including policies on SSI designation.

(Sec. 535) Prohibits the use of funds appropriated by this Act to change the name of the Coast Guard Station "Group St. Petersburg."

Rescinds certain unobligated balances available in the DHS Working Capital Fund.

Title II: Security, Enforcement, and Investigations - Makes FY2006 appropriations for: (1) the Office of the Under Secretary for Border and Transportation Security, including expenses of the U.S. Visitor and Immigrant Status Indicator Technology project (US-VISIT); (2) Customs and Border Protection (CBP), including enforcement of laws relating to border security, immigration, customs, and agricultural inspections and regulatory activities related to plant and animal imports, customs and border protection automated systems, and air and marine interdiction; (3) Immigration and Customs Enforcement (ICE), including Federal Air Marshals, the Federal Protective Service, and immigration and customs enforcement automated systems; (4) the Transportation Security Administration (TSA); (5) the Coast Guard; and (6) the U.S. Secret Service.

Title III: Preparedness and Recovery - Makes FY2006 appropriations for: (1) the Office of State and Local Government Coordination and Preparedness, including grants to State and local governments for terrorism prevention activities (with allocations for formula-based grants, law enforcement terrorism prevention grants, discretionary transportation and infrastructure grants for use in high-threat, high density urban areas and for port security, trucking industry security, and transit security, and buffer zone protection plan grants), firefighter assistance grants, and emergency management performance grants; (2) reimbursement of Federal agencies for the costs of providing support to counter, investigate, or respond to unexpected threats or acts of terrorism; (3) emergency preparedness and response, including the Office of the Under Secretary for Emergency Preparedness and Response, public health programs, disaster relief, the disaster assistance direct loan program, the Flood Map Modernization Fund, the National Flood Insurance Fund, the National Flood Mitigation Fund, the National PreDisaster Mitigation Fund, and an emergency food and shelter program.

Requires aggregate charges assessed during FY2006 for the Radiological Emergency Preparedness Program to be not less than 100% of the necessary amounts anticipated by DHS.

Title IV: Research and Development, Training, Assessments, and Services - Makes FY2006 appropriations for: (1) U.S. Citizenship and Immigration Services; (2) the Federal Law Enforcement Training Center; (3) information analysis and infrastructure protection, including for the immediate Office of the Under Secretary for Information Analysis and Infrastructure Protection and the management and administration of programs and activities; and (4) the immediate Office of the Under Secretary for Science and Technology, management and administration of programs and activities, and science and technology research, including for advanced research projects.

Title V: General Provisions - (Sec. 502) Prohibits the use of appropriated funds for payments to the Working Capital Fund, except for certain activities and amounts, with any additional activities and amounts to be approved by the Committees on Appropriations of the Senate and the House of Representatives.

(Sec. 505) Deems funds made available by this Act for intelligence activities to be specifically authorized by Congress during FY2006 until the enactment of an Act authorizing intelligence activities for FY2006.

(Sec. 508) Requires the Director of the Federal Law Enforcement Training Center to schedule basic and/or advanced law enforcement training at all four training facilities under Center control to ensure that they are operated at the highest capacity throughout the fiscal year.

(Sec. 510) Prohibits the use of funds in this Act in contravention of applicable provisions of the Buy American Act.

(Sec. 511) Directs the Secretary of Homeland Security to research, develop, and procure certified systems to inspect and screen air cargo on passenger aircraft at the earliest date possible. Requires the Secretary, until such technology is procured and installed, to take all possible actions to enhance the known shipper program to prohibit high-risk cargo from being transported on passenger aircraft, and continue to increase the level of air cargo that is inspected beyond the level mandated.

(Sec. 513) Applies TSA acquisition management system to the acquisition of services, as well as equipment, supplies, and materials.

(Sec. 514) Prohibits the obligation of funds for deployment or implementation of the Secure Flight program or other follow on or successor passenger prescreening program, on other than a test basis, until the Secretary has certified and the Government Accountability Office has reported that specified requirements have been met.

(Sec. 515) Prohibits the use of funds made available in this Act to amend the oath of allegiance required for naturalization under the Immigration and Nationality Act.

(Sec. 516) Prohibits the use of funds appropriated by this Act to process or approve a competition under Office of Management and Budget Circular A-76 for services provided as of June 1, 2004, by employees of the DHS Bureau of Citizenship and Immigration Services who are known as Immigration Information Officers, Contact Representatives, or Investigative Assistants.

(Sec. 517) Prohibits the use of funds appropriated to the U.S. Secret Service for the protection of a federal agency head other than the Secretary of Homeland Security. Authorizes the Director of the U.S. Secret Service to enter into an agreement to perform such service on a fully reimbursable basis.

(Sec. 518) Names the DHS processing and data storage facilities at the John C. Stennis Space Center the National Center for Critical Information Processing and Storage.

Rescinds certain unobligated balances available in the DHS Working Capital Fund.

Title II: Security, Enforcement, and Investigations - Makes FY2006 appropriations for: (1) the Office of the Under Secretary for Border and Transportation Security, including expenses of the U.S. Visitor and Immigrant Status Indicator Technology project (US-VISIT); (2) Customs and Border Protection (CBP), including enforcement of laws relating to border security, immigration, customs, and agricultural inspections and regulatory activities related to plant and animal imports, customs and border protection automated systems, and air and marine interdiction; (3) Immigration and Customs Enforcement (ICE), including Federal Air Marshals, the Federal Protective Service, and immigration and customs enforcement automated systems; (4) the Transportation Security Administration (TSA); (5) the Coast Guard; and (6) the U.S. Secret Service.

Title III: Preparedness and Recovery - Makes FY2006 appropriations for: (1) the Office of state and Local Government Coordination and Preparedness, including grants to state and local governments for terrorism prevention activities (with allocations for formula-based grants, law enforcement terrorism prevention grants, discretionary transportation and infrastructure grants for use in high-threat, high density urban areas and for port security, trucking industry security, and transit security, and buffer zone protection plan grants), firefighter assistance grants, and emergency management performance grants; (2) reimbursement of Federal agencies for the costs of providing support to counter, investigate, or respond to unexpected threats or acts of terrorism; (3) emergency preparedness and response, including the Office of the Under Secretary for Emergency Preparedness and Response, public health programs, disaster relief, the disaster assistance direct loan program, the Flood Map Modernization Fund, the National Flood Insurance Fund, the National Flood Mitigation Fund, the National PreDisaster Mitigation Fund, and an emergency food and shelter program.

States that the aggregate charges assessed during FY2006 for the Radiological Emergency Preparedness Program shall not be less than 100% of the necessary amounts anticipated by DHS.

Title IV: Research and Development, Training, Assessments, and Services - Makes FY2006 appropriations for: (1) U.S. Citizenship and Immigration Services; (2) the Federal Law Enforcement Training Center; (3) information analysis and infrastructure protection, including for the immediate Office of the Under Secretary for Information Analysis and Infrastructure Protection and the management and administration of programs and activities; and (4) the immediate Office of the Under Secretary for Science and Technology, management and administration of programs and activities, and science and technology research, including for advanced research projects.

Title V: General Provisions - (Sec. 502) Prohibits the use of appropriated funds from being used to make payments to the Working Capital Fund, except for certain activities and amounts, with any additional activities and amounts to be approved by the Committees on Appropriations of the Senate and the House of Representatives.

(Sec. 505) Deems funds made available by this Act for intelligence activities to be specifically authorized by Congress during FY2006 until the enactment of an Act authorizing intelligence activities for FY2006.

(Sec. 508) Requires the Director of the Federal Law Enforcement Training Center to schedule basic and/or advanced law enforcement training at all four training facilities under Center control to ensure that they are operated at the highest capacity throughout the fiscal year.

(Sec. 510) Prohibits the use of funds in this Act in contravention of applicable provisions of the Buy America Act.

(Sec. 511) Directs the Secretary of Homeland Security to research, develop, and procure certified systems to inspect and screen air cargo on passenger aircraft at the earliest date possible. Requires the Secretary, until such technology is procured and installed, to take all possible actions to enhance the known shipper program to prohibit high-risk cargo from being transported on passenger aircraft, and continue to increase the level of air cargo that is inspected beyond the level mandated.

(Sec. 513) Applies TSA acquisition management system to the acquisition of services, as well as equipment, supplies, and materials.

(Sec. 514) Prohibits the obligation of funds for deployment or implementation of the Secure Flight program or other follow on or successor passenger prescreening program, on other than a test basis, until the Secretary has certified and the Government Accountability Office has reported that specified requirements have been met.

(Sec. 515) Prohibits the use of funds made available in this Act to amend the oath of allegiance required for naturalization under the Immigration and Nationality Act.

(Sec. 516) Prohibits the use of funds appropriated by this Act to process or approve a competition under Office of Management and Budget Circular A-76 for services provided as of June 1, 2004, by employees of the DHS Bureau of Citizenship and Immigration Services who are known as Immigration Information Officers, Contact Representatives, or Investigative Assistants.

(Sec. 517) Prohibits the use of funds appropriated to the U.S. Secret Service from being made available for the protection of the head of a federal agency other than the Secretary of Homeland Security. Authorizes the Director of the U.S. Secret Service to enter into an agreement to perform such service on a fully reimbursable basis.

(Sec. 518) Names the DHS processing and data storage facilities at the John C. Stennis Space Center the National Center for Critical Information Processing and Storage.

(Sec. 519) Expresses the sense of the Senate that: (1) this Nation cannot thoroughly address its security without recognizing the reality of terrorists taking advantage of inadequacies in border security along the border between the United States and Mexico; (2) every effort should be made to increase the technology and efficiency in preventing these individuals from entering the United States across the Mexican border; (3) the Mexican Government has an obligation to secure its side of the border; and (4) it must commit to addressing inadequacies in its own domestic and border security policies, which are contributing to the present dilemma in border security.

(Sec. 520) Appropriates $1.5 billion to the Department of Veterans Affairs as an emergency requirement for FY2005 for medical services provided by the Veterans Health Administration.

(Sec. 521) Requires the DHS Office of Inspector General to report to specified House and Senate Committees on the steps taken to comply with the recommendations of the Inspector General's Report on the Port Security Grant Program (OIG-05-10).

(Sec. 522) Directs the Secretary to survey state and local government emergency officials to identify problems relating to the effectiveness and user-friendliness of programs in which DHS interacts with state and local officials. Requires a report to relevant congressional committees.

(Sec. 523) Directs the Secretary to conduct quadrennial homeland defense reviews.

(Sec. 524) Expresses the sense of the Senate that: (1) DHS is urged to invest in research to promote tunnel rail safety as well as training to ensure first responders are prepared for rail tunnel emergencies; and (2) employing existing federal facilities in this effort can result in efficiencies and permit this important research to proceed at decreased cost to the taxpayer and with minimal interference with ongoing passenger and freight rail traffic.

(Sec. 525) Encourages the Secretary, upon completion of the DHS operational testing of man portable air defense (MANPAD) countermeasure systems for commercial aircraft, to designate an agency within DHS as responsible for managing the procurement and installation of such systems. Authorizes the Secretary to use any unobligated funds provided under title I to establish an office within the designated agency for that purpose.

(Sec. 526) Directs the Secretary, acting through the Director of the Federal Emergency Management Agency (FEMA), to provide to the Subcommittee on Homeland Security of the Committee on Appropriations of the Senate: (1) a detailed list of all associated costs incurred by New York City, the State of New York, and any other entity or organization established by New York City or the State of New York as a result of the terrorist attacks of September 11, 2001, that were paid using funds made available by Congress; (2) a detailed description of the amounts of funds made available after the such attacks that remain unexpended; (3) the accounts containing those unexpended funds; and (4) a detailed description of any plans for expenditure or obligation of those unexpended funds.

(Sec. 527) Directs the Secretary to assess and report to specified congressional committees on: (1) the vulnerability posed to high risk areas and facilities from general aviation aircraft that could be stolen or used as or armed with a weapon; (2) the security vulnerabilities at general aviation airports that would permit general aviation aircraft to be stolen; (3) low-cost, high-performance technology that could be used to track easily general aviation aircraft that could otherwise fly undetected; (4) the feasibility of implementing security measures that would disable general aviation aircraft while parked on the ground to prevent theft; (5) the feasibility of background checks on individuals working at general aviation airports who have access to aircraft or flight line activities; (6) the threat posed to high population areas, nuclear facilities, key infrastructure, military bases, and transportation infrastructure by stolen or hijacked general aviation aircraft, especially if armed with weapons or explosives; (7) existing security precautions at general aviation airports to prevent breaches of the flight line and perimeter; (8) whether unmanned air traffic control towers provide a security or alert weakness; and (9) additional measures that should be adopted to ensure the security of general aviation aircraft.

(Sec. 528) Requires the head of each DHS department or agency engaged in any activity to use or develop data-mining technology to report to Congress on all such activities.

(Sec. 529) Prohibits the use of funds made available in this Act for items identified as wasteful.

(Sec. 530) Directs the Secretary to designate the Natrona International Airport in Casper, Wyoming, as an airport at which certain private aircraft arriving from a foreign area may land for processing by the U.S. Customs and Border Protection. Prohibits treatment of such airport as a user fee airport.

(Sec. 531) Expresses the sense of the Senate that FEMA or any other organization within DHS should continue to coordinate with the American Red Cross in developing a mass care plan for the United States in response to a catastrophic event.

(Sec. 532) Expresses the sense of the Congress that: (1) the information requested in a certain required report to Congress on performance indicators and measures for progress toward military and political stability in Iraq is critical; (2) the report should be provided by the Department of Defense as soon as possible; and (3) the Secretary of Defense should communicate to Congress and the American people why the report was not submitted to Congress by the original deadline.

(Sec. 533) Expresses the sense of the Senate that the Congress should pass legislation establishing enforceable federal standards to protect against a terrorist attack on chemical facilities within the United States.

(Sec. 534) Directs the Secretary, acting through the Under Secretary for Emergency Preparedness and Response, to provide clear, concise, and uniform guidelines for the reimbursement to any county or government entity affected by a hurricane of the costs of hurricane debris removal.

(Sec. 535) Directs the Secretary to report to specified congressional committees on any changes to federal emergency preparedness and response policies and practices made as a result of the report of the Inspector General, dated May 20, 2005, relating to the FEMA individual and household program in Miami-Dade County, Florida, in response to Hurricane Frances.

(Sec. 536) Expresses the sense of the Senate that the Secretary should study the feasibility of leveraging existing FM broadcast radio infrastructure to provide a first alert, encrypted multi-point emergency messaging system for emergency response using proven technology.

(Sec. 537) Requires the Secretary, acting through the Under Secretary for Emergency Preparedness, to propose new inspection guidelines that prohibit inspectors from entering into a contract with any individual or entity for whom the inspector performs an inspection for purposes of determining eligibility for FEMA assistance.

(Sec. 538) Prohibits the use of funds appropriated under this Act to promulgate regulations to implement the plan developed pursuant to the 9/11 Commission Implementation Act of 2004 to limit U.S. citizens to a passport as the exclusive document to be presented upon entry into the United States from Canada by land.

(Sec. 539) Directs the Comptroller General to study and report to Congress on the six occasions in which the Homeland Security Advisory System was raised to Code Orange prior to July 2005.

(Sec. 540) Expresses the sense of the Senate that the Congress should pass bipartisan legislation to address nuclear power plant security prior to the August recess.

(Sec. 541) Expresses the sense of the Senate that in the assessment of threat as it relates to the dispersal of DHS funding the Secretary should consider tourism destinations that attract tens of millions of visitors annually as potentially high risk targets.

Title VI: Homeland Security Grant Enhancement - Homeland Security Grant Enhancement Act of 2005 - (Sec. 602) Amends the Homeland Security Act of 2002 to require the Secretary to establish the Interagency Committee to Coordinate and Streamline Homeland Security Grant Programs to promote the coordination of homeland security grant programs throughout the federal government.

(Sec. 603) Creates the position of Executive Director to head the DHS Office for State and Local Government Coordination and Preparedness (OSLGCP). Reconstitutes the DHS Office for Domestic Preparedness (currently, within the Directorate of Border and Transportation Security) as a component of OSLGCP, and gives it additional responsibility for managing the Homeland Security Information Clearinghouse. Establishes the Clearinghouse within OSLGCP to provide states, local governments, and emergency response providers with information regarding: (1) homeland security grants; (2) technical assistance; (3) best practices; and (4) the use of federal funds.

(Sec. 604) Preserves specified federal grant programs for traditional missions of state and local law enforcement, firefighters, ports, emergency medical services, or public health missions that existed prior to September 11, 2001.

Directs the Secretary to establish clearly defined essential capabilities for state and local governments with specificity, flexibility, measurability, and comprehensiveness. Requires the Secretary to establish a Task Force on Essential Capabilities for First Responders.

Establishes a discretionary Threat-Based Homeland Security Grant Program for states and eligible metropolitan regions. Requires the use of grants under the program to address homeland security matters concerning terrorism or catastrophic events, related capacity building, or otherwise address shortfalls in essential capabilities. Prohibits their use to supplant ongoing emergency response expenses or general protective measures, or to construct buildings or other physical facilities (with specified exceptions).

Authorizes the use of such grants to achieve essential capabilities through: (1) developing state or regional plans or risk assessments, and state, regional, or local mutual aid agreements; (2) purchasing, upgrading, or maintaining necessary equipment; (3) conducting emergency preparedness exercises for state and local first responders; and (4) promoting related training.

Requires any state applying for a grant to have a three-year state homeland security plan approved by the Secretary.

Prescribes grant fund allocation requirements, specifying a sliding scale baseline, an urban area security initiative distribution, and a threat-based distribution to states, as well as funding for local governments and first responders.

Authorizes appropriations for FY2006 and following fiscal years.

Directs the Secretary to support the development of, promulgate, and update as necessary national voluntary consensus standards for the performance, use, and validation of first responder equipment for purposes of assessing equipment-related grant applications.

Requires the Bureau of Customs and Border Protection (CBP) to report to Congress on: (1) whether CBP methodologies and technologies used to screen for and detect chemical, nuclear, biological, and radiological weapons in municipal solid waste are as effective as those used to screen for such materials in other items of commerce entering the United States by commercial motor vehicle transport; and (2) actions CBP will take to achieve comparability, if such methodologies and technologies are less effective.

Requires the Secretary, if CBP fails fully to implement actions to achieve comparability within a specified time frame, to deny entry into the United States to commercial motor vehicles carrying municipal solid waste until the Secretary certifies to Congress that screening of such waste comparable to that used to screen in other items of commerce has been achieved.

(Sec. 605) Establishes in DHS an International Border Community Interoperable Communications Demonstration Project to: (1) address the interoperable communications needs of police officers, firefighters, emergency medical technicians, the National Guard, and other emergency response providers; (2) foster interoperable communications among domestic government agencies and their counterparts in Canada or Mexico; (3) identify common international cross-border frequencies; (4) foster standardization of interoperable communications equipment; (5) provide training and equipment to enable emergency response providers to deal with environmentally varied threats and contingencies; and (6) identify and secure appropriate joint-use equipment. Directs the Secretary to select no fewer than six communities to participate in the project, to be divided equally between the northern and southern border.

Title II: Security, Enforcement, and Investigations - Makes FY2006 appropriations for: (1) the U.S. Visitor and Immigrant Status Indicator Technology (U.S.-VISIT) project; (2) Customs and Border Protection (CBP), including customs and border protection automated systems, air and marine interdiction, and construction; (3) Immigration and Customs Enforcement (ICE); (4) the Federal Protective Service, including immigration and customs enforcement automated systems, and construction; (4) the Transportation Security Administration (TSA), including surface transportation security, transportation vetting and credentialing, transportation security support, and Federal Air Marshals; (5) the Coast Guard, including environmental compliance and restoration, Coast Guard Reserve training, acquisition, construction, and improvements, alteration of bridges, research, development, test, and evaluation, and retired pay; and (6) the U.S. Secret Service, including acquisition, construction, and improvements.

Title III: Preparedness and Recovery - Makes FY2006 appropriations for: (1) the Office of the Under Secretary for Preparedness, the Office of the Chief Medical Officer, and the Office of National Capital Regional Coordination; (2) the Office for Domestic Preparedness, including grants to state and local governments for terrorism prevention activities, firefighter assistance grants, and emergency management performance grants, the U.S. Fire Administration and training, infrastructure protection and information security, and the Counterterrorism Fund; (3) the Federal Emergency Management Agency (FEMA), including preparedness, mitigation, response, and recovery, public health programs, disaster relief, the disaster assistance direct loan program, the Flood Map Modernization Fund, the National Flood Insurance Fund, the National Flood Mitigation Fund, the National Pre-Disaster Mitigation Fund, and an emergency food and shelter program.

States that the aggregate charges assessed during FY2006 for the Radiological Emergency Preparedness Program shall not be less than 100% of the necessary amounts anticipated by DHS.

Title IV: Research and Development, Training, and Services - Makes FY2006 appropriations for: (1) U.S. Citizenship and Immigration Services; (2) the Federal Law Enforcement Training Center, including acquisition, construction, and improvements; and (3) the Office of the Under Secretary for Science and Technology, including science and technology research, development, acquisition, and operations.

Title V: General Provisions - (Sec. 504) Prohibits the use of appropriated funds to make payments to the Working Capital Fund, except for certain activities and amounts.

(Sec. 506) Deems funds made available by this Act for intelligence activities to be specifically authorized by Congress during FY2006 until the enactment of an Act authorizing such activities for FY2006.

(Sec. 507) Directs the Federal Law Enforcement Training Center to lead the federal law enforcement training accreditation process, to include representatives from the federal law enforcement community and nonfederal accreditation experts involved in law enforcement training, to continue the implementation of measuring and assessing the quality and effectiveness of federal law enforcement training programs, facilities, and instructors.

(Sec. 510) Requires the Director of the Federal Law Enforcement Training Center to schedule basic and/or advanced law enforcement training at all four training facilities under Center control to ensure that they are operated at the highest capacity throughout the fiscal year.

(Sec. 512) Prohibits the use of funds in this Act in contravention of the Buy American Act.

(Sec. 513) Directs the Secretary to ensure that DHS is in compliance with the requirement in the Department of Homeland Security Appropriations Act, 2005 that the Secretary amend Security Directives and programs to at least triple the percentage of cargo inspected on passenger aircraft. Requires the Secretary to report to specified congressional committees biweekly beginning on October 1, 2005, on any reason for noncompliance.

Directs the Secretary to take all possible actions, including the procurement of certified systems to inspect and screen air cargo on passenger aircraft, to increase the level of air cargo inspected beyond that mandated.

(Sec. 515) Applies TSA acquisition management system to the acquisition of services, as well as equipment, supplies, and materials.

(Sec. 516) Transfers authority to conduct background investigations from the Office of Personnel Management to DHS.

(Sec. 517) Exempts funds appropriated under the State and Local Programs heading under Title III of this Act from the Cash Management Improvement Act of 1990.

(Sec. 518) Prohibits the obligation of funds for deployment or implementation of the Secure Flight program or other follow on or successor passenger prescreening program, on other than a test basis, until the Secretary has certified and the Government Accountability Office (GAO) has reported that specified requirements have been met.

(Sec. 519) Prohibits the use of funds made available in this Act to amend the oath of allegiance required for naturalization under the Immigration and Nationality Act.

(Sec. 520) Prohibits the use of funds appropriated by this Act to process or approve a competition under Office of Management and Budget Circular A-76 for services provided as of June 1, 2004, by employees of the DHS Bureau of Citizenship and Immigration Services who are known as Immigration Information Officers, Contact Representatives, or Investigative Assistants.

(Sec. 521) Prohibits the availability of funds appropriated by this Act to maintain the U.S. Secret Service as anything but a distinct entity within DHS. Prohibits the use of such funds to merge the Secret Service with any other DHS function, cause any personnel and operational elements to report to an individual other than the Director of the U.S. Secret Service, or cause the Director to report directly to any individual other than the Secretary.

(Sec. 522) Prohibits the availability of funds appropriated to the U.S. Secret Service for the protection of the head of a federal agency other than the Secretary, unless the Director is fully reimbursed.

(Sec. 523) Names the DHS processing and data storage facilities at the John C. Stennis Space Center the National Center for Critical Information Processing and Storage.

(Sec. 524) Directs the Secretary to develop standards and protocols for increasing the use of explosive detection equipment to screen air cargo when appropriate.

(Sec. 525) Directs the TSA to utilize existing checked baggage explosive detection equipment and screeners to screen cargo carried on passenger aircraft to the greatest extent practicable at each airport. Directs TSA to report monthly to specified congressional committees on the amount of cargo carried on passenger aircraft that was screened.

(Sec. 526) Prohibits the use of any funds available for the transportation worker identification credential program to develop a personalized system that is decentralized or a card production capability that does not utilize an existing government card production facility.

(Sec. 527) Rescinds $78,630,689 for integrated Deepwater System 110-123-foot patrol boats conversion. Reappropriates such funds for the service life extension of the current Island Class patrol boat fleet and accelerated design and and production of the Fast Response Cutter.

(Sec. 528) Requires the Secretary to utilize the Transportation Security Clearinghouse as the central identity management system for the deployment and operation of the registered traveler program and the transportation worker identification credential program for the purposes of collecting and aggregating biometric data necessary for background vetting.

(Sec. 529) Prohibits the use of funds in this Act by any person but the privacy officer appointed under the Homeland Security Act of 2002 to alter, direct that changes be made to, delay, or prohibit the transmission of a privacy officer report to Congress.

(Sec. 530) Prohibits the availability of any funds to pay the salary of any employee serving as a contracting officer's technical representative (COTR), or anyone acting in a similar or like capacity, who has not received COTR training.

(Sec. 531) Makes any funds appropriated or transferred to TSA "Aviation Security" and "Administration" in FY2004 and 2005, which are recovered or deobligated, available only for procurement and installation of explosive detection systems for air cargo, baggage, and checkpoint screening systems.

(Sec. 532) Requires the Secretary to survey all ports of entry in the United States and designate an airport as a port of entry in each state that does not have one.

(Sec. 533) Directs the Secretary to consider eligible under the Federal Emergency Management Agency (FEMA) Public Assistance Program the costs sufficient to enable the City of Paso Robles, California, to repair and upgrade all elements of the Carnegie Library damaged (or undamaged) by the 2003 San Simeon earthquake so that the library is brought into conformance with all local code requirements for new construction.

(Sec. 534) Directs the Secretary to consider eligible under the FEMA Public Assistance Program costs for the damage to canals and wooden flumes, incurred during a 1996 storm and subsequent mudslide in El Dorado County, California, to the El Dorado Irrigation District, based on 50% of the costs of the Improved Project for the Mill Creek to Bull Creek tunnel proposed in a November 2001 Carleton Engineering Report.

(Sec. 535) Directs the Secretary to consider eligible under the FEMA Public Assistance Program the costs sufficient to enable replacement of research and education materials and library collections, and for other non-covered losses, at the University of Hawaii Manoa campus, Hawaii, resulting from an October 30, 2004, flood event.

(Sec. 536) Amends the Immigration and Nationality Act to authorize H2A visas to nonimmigrant aliens coming temporarily to the United States to perform the pressing of apples for cider on a farm.

(Sec. 537) Directs the Secretary to provide that each office within DHS that handles documents marked as Sensitive Security Information (SSI) has at least one employee with authority to coordinate and make determinations on the agency's behalf that such documents meet the criteria for marking as SSI. Requires reports to Congress of DHS SSI policies, auditing, and accountability.

(Sec. 538) Appropriates $40 million for discretionary grants to states to implement the REAL ID Act of 2005, subject to congressional approval of the implementation plan. Earmarks a portion of such funds for availability to states for pilot projects on integrating hardware, software, and information management systems.

(Sec. 539) Extends the authorization of the Working Capital Fund through FY2006.

(Sec. 540) Directs the Secretary to impose a fee for the registered traveler program.

(Sec. 541) Extends liability protection to certain persons who report a situation, activity or incident, if they have completed a security awareness training course approved by or operating under a cooperative agreement with DHS, and are enrolled in a program recognized or acknowledged by an Information Sharing and Analysis Center.

(Sec. 542) Rescinds $15 million from the unobligated balances available in the DHS Working Capital Fund.

(Sec. 543) Rescinds $5.5 million from unobligated balances previously appropriated for TSA "Aviation Security."

(Sec. 544) Rescinds $6,369,118 in appropriations for the Coast Guard.

(Sec. 545) Rescinds $8 million from unobligated balances previously appropriated to the Counterterrorism Fund.

(Sec. 546) Rescinds $20 million from unobligated balances previously appropriated to Science and Technology for research, development, acquisition, and operations.

(Sec. 547) Declares that an airport operator shall not be liable for any claims for damages filed in state or federal court relating to: (1) its decision to apply or not to apply for the security screening pilot program; and (2) any act of negligence, gross negligence, or intentional wrongdoing by a qualified private screening company (or its employees) while acting under a DHS contract, or by federal employees providing passenger and property security screening services at the airport.

States that an airport operator shall not be relieved from liability for its own acts or omissions related to its security responsibilities. Prohibits an airport operator from relieving any qualified private screening company or its employees from any liability related to its own acts of negligence, gross negligence, or intentional wrongdoing.

(Sec. 548) Requires the weekly disaster relief report required by the Second Emergency Supplemental Appropriations Act to Meet Immediate Needs Arising From the Consequences of Hurricane Katrina, 2005 to include specified details on certain allocations, obligations, expenditures, and credit card purchases.

Department of Homeland Security Appropriations Act, 2006 - Title I: Departmental Management and Operations - Makes appropriations for the Department of Homeland Security (DHS) for FY2006 for: (1) the Office of the Secretary of Homeland Security (Secretary) and executive management; (2) the Office of Screening Coordination and Operations; (3) Office of the Under Secretary for Management; (4) the Office of the Chief Financial Officer; (5) the Office of the Chief Information Officer; (6) analysis and operations; and (7) the Office of Inspector General.

Title II: Security, Enforcement, and Investigations - Makes FY2006 appropriations for: (1) the U.S. Visitor and Immigrant Status Indicator Technology (U.S.-VISIT) project; (2) Customs and Border Protection (CBP), including customs and border protection automated systems, air and marine interdiction, and construction; (3) Immigration and Customs Enforcement (ICE); (4) the Federal Protective Service, including immigration and customs enforcement automated systems, and construction; (4) the Transportation Security Administration (TSA), including surface transportation security, transportation vetting and credentialing, transportation security support, and Federal Air Marshals; (5) the Coast Guard, including environmental compliance and restoration, Coast Guard Reserve training, acquisition, construction, and improvements, alteration of bridges, research, development, test, and evaluation, and retired pay; and (6) the U.S. Secret Service, including acquisition, construction, and improvements.

Title III: Preparedness and Recovery - Makes FY2006 appropriations for: (1) the Office of the Under Secretary for Preparedness, the Office of the Chief Medical Officer, and the Office of National Capital Regional Coordination; (2) the Office for Domestic Preparedness, including grants to state and local governments for terrorism prevention activities, firefighter assistance grants, and emergency management performance grants, the U.S. Fire Administration and training, infrastructure protection and information security, and the Counterterrorism Fund; (3) the Federal Emergency Management Agency (FEMA), including preparedness, mitigation, response, and recovery, public health programs, disaster relief, the disaster assistance direct loan program, the Flood Map Modernization Fund, the National Flood Insurance Fund, the National Flood Mitigation Fund, the National Pre-Disaster Mitigation Fund, and an emergency food and shelter program.

States that the aggregate charges assessed during FY2006 for the Radiological Emergency Preparedness Program shall not be less than 100% of the necessary amounts anticipated by DHS.

Title IV: Research and Development, Training, and Services - Makes FY2006 appropriations for: (1) U.S. Citizenship and Immigration Services; (2) the Federal Law Enforcement Training Center, including acquisition, construction, and improvements; and (3) the Office of the Under Secretary for Science and Technology, including science and technology research, development, acquisition, and operations.

Title V: General Provisions - (Sec. 504) Prohibits the use of appropriated funds to make payments to the Working Capital Fund, except for certain activities and amounts.

(Sec. 506) Deems funds made available by this Act for intelligence activities to be specifically authorized by Congress during FY2006 until the enactment of an Act authorizing such activities for FY2006.

(Sec. 507) Directs the Federal Law Enforcement Training Center to lead the federal law enforcement training accreditation process, to include representatives from the federal law enforcement community and nonfederal accreditation experts involved in law enforcement training, to continue the implementation of measuring and assessing the quality and effectiveness of federal law enforcement training programs, facilities, and instructors.

(Sec. 510) Requires the Director of the Federal Law Enforcement Training Center to schedule basic and/or advanced law enforcement training at all four training facilities under Center control to ensure that they are operated at the highest capacity throughout the fiscal year.

(Sec. 512) Prohibits the use of funds in this Act in contravention of the Buy American Act.

(Sec. 513) Directs the Secretary to ensure that DHS is in compliance with the requirement in the Department of Homeland Security Appropriations Act, 2005 that the Secretary amend Security Directives and programs to at least triple the percentage of cargo inspected on passenger aircraft. Requires the Secretary to report to specified congressional committees biweekly beginning on October 1, 2005, on any reason for noncompliance.

Directs the Secretary to take all possible actions, including the procurement of certified systems to inspect and screen air cargo on passenger aircraft, to increase the level of air cargo inspected beyond that mandated.

(Sec. 515) Applies TSA acquisition management system to the acquisition of services, as well as equipment, supplies, and materials.

(Sec. 516) Transfers authority to conduct background investigations from the Office of Personnel Management to DHS.

(Sec. 517) Exempts funds appropriated under the State and Local Programs heading under Title III of this Act from the Cash Management Improvement Act of 1990.

(Sec. 518) Prohibits the obligation of funds for deployment or implementation of the Secure Flight program or other follow on or successor passenger prescreening program, on other than a test basis, until the Secretary has certified and the Government Accountability Office (GAO) has reported that specified requirements have been met.

(Sec. 519) Prohibits the use of funds made available in this Act to amend the oath of allegiance required for naturalization under the Immigration and Nationality Act.

(Sec. 520) Prohibits the use of funds appropriated by this Act to process or approve a competition under Office of Management and Budget Circular A-76 for services provided as of June 1, 2004, by employees of the DHS Bureau of Citizenship and Immigration Services who are known as Immigration Information Officers, Contact Representatives, or Investigative Assistants.

(Sec. 521) Prohibits the availability of funds appropriated by this Act to maintain the U.S. Secret Service as anything but a distinct entity within DHS. Prohibits the use of such funds to merge the Secret Service with any other DHS function, cause any personnel and operational elements to report to an individual other than the Director of the U.S. Secret Service, or cause the Director to report directly to any individual other than the Secretary.

(Sec. 522) Prohibits the availability of funds appropriated to the U.S. Secret Service for the protection of the head of a federal agency other than the Secretary, unless the Director is fully reimbursed.

(Sec. 523) Names the DHS processing and data storage facilities at the John C. Stennis Space Center the National Center for Critical Information Processing and Storage.

(Sec. 524) Directs the Secretary to develop standards and protocols for increasing the use of explosive detection equipment to screen air cargo when appropriate.

(Sec. 525) Directs the TSA to utilize existing checked baggage explosive detection equipment and screeners to screen cargo carried on passenger aircraft to the greatest extent practicable at each airport. Directs TSA to report monthly to specified congressional committees on the amount of cargo carried on passenger aircraft that was screened.

(Sec. 526) Prohibits the use of any funds available for the transportation worker identification credential program to develop a personalized system that is decentralized or a card production capability that does not utilize an existing government card production facility.

(Sec. 527) Rescinds $78,630,689 for integrated Deepwater System 110-123-foot patrol boats conversion. Reappropriates such funds for the service life extension of the current Island Class patrol boat fleet and accelerated design and and production of the Fast Response Cutter.

(Sec. 528) Requires the Secretary to utilize the Transportation Security Clearinghouse as the central identity management system for the deployment and operation of the registered traveler program and the transportation worker identification credential program for the purposes of collecting and aggregating biometric data necessary for background vetting.

(Sec. 529) Prohibits the use of funds in this Act by any person but the privacy officer appointed under the Homeland Security Act of 2002 to alter, direct that changes be made to, delay, or prohibit the transmission of a privacy officer report to Congress.

(Sec. 530) Prohibits the availability of any funds to pay the salary of any employee serving as a contracting officer's technical representative (COTR), or anyone acting in a similar or like capacity, who has not received COTR training.

(Sec. 531) Makes any funds appropriated or transferred to TSA "Aviation Security" and "Administration" in FY2004 and 2005, which are recovered or deobligated, available only for procurement and installation of explosive detection systems for air cargo, baggage, and checkpoint screening systems.

(Sec. 532) Requires the Secretary to survey all ports of entry in the United States and designate an airport as a port of entry in each state that does not have one.

(Sec. 533) Directs the Secretary to consider eligible under the Federal Emergency Management Agency (FEMA) Public Assistance Program the costs sufficient to enable the City of Paso Robles, California, to repair and upgrade all elements of the Carnegie Library damaged (or undamaged) by the 2003 San Simeon earthquake so that the library is brought into conformance with all local code requirements for new construction.

(Sec. 534) Directs the Secretary to consider eligible under the FEMA Public Assistance Program costs for the damage to canals and wooden flumes, incurred during a 1996 storm and subsequent mudslide in El Dorado County, California, to the El Dorado Irrigation District, based on 50% of the costs of the Improved Project for the Mill Creek to Bull Creek tunnel proposed in a November 2001 Carleton Engineering Report.

(Sec. 535) Directs the Secretary to consider eligible under the FEMA Public Assistance Program the costs sufficient to enable replacement of research and education materials and library collections, and for other non-covered losses, at the University of Hawaii Manoa campus, Hawaii, resulting from an October 30, 2004, flood event.

(Sec. 536) Amends the Immigration and Nationality Act to authorize H2A visas to nonimmigrant aliens coming temporarily to the United States to perform the pressing of apples for cider on a farm.

(Sec. 537) Directs the Secretary to provide that each office within DHS that handles documents marked as Sensitive Security Information (SSI) has at least one employee with authority to coordinate and make determinations on the agency's behalf that such documents meet the criteria for marking as SSI. Requires reports to Congress of DHS SSI policies, auditing, and accountability.

(Sec. 538) Appropriates $40 million for discretionary grants to states to implement the REAL ID Act of 2005, subject to congressional approval of the implementation plan. Earmarks a portion of such funds for availability to states for pilot projects on integrating hardware, software, and information management systems.

(Sec. 539) Extends the authorization of the Working Capital Fund through FY2006.

(Sec. 540) Directs the Secretary to impose a fee for the registered traveler program.

(Sec. 541) Extends liability protection to certain persons who report a situation, activity or incident, if they have completed a security awareness training course approved by or operating under a cooperative agreement with DHS, and are enrolled in a program recognized or acknowledged by an Information Sharing and Analysis Center.

(Sec. 542) Rescinds $15 million from the unobligated balances available in the DHS Working Capital Fund.

(Sec. 543) Rescinds $5.5 million from unobligated balances previously appropriated for TSA "Aviation Security."

(Sec. 544) Rescinds $6,369,118 in appropriations for the Coast Guard.

(Sec. 545) Rescinds $8 million from unobligated balances previously appropriated to the Counterterrorism Fund.

(Sec. 546) Rescinds $20 million from unobligated balances previously appropriated to Science and Technology for research, development, acquisition, and operations.

(Sec. 547) Declares that an airport operator shall not be liable for any claims for damages filed in state or federal court relating to: (1) its decision to apply or not to apply for the security screening pilot program; and (2) any act of negligence, gross negligence, or intentional wrongdoing by a qualified private screening company (or its employees) while acting under a DHS contract, or by federal employees providing passenger and property security screening services at the airport.

States that an airport operator shall not be relieved from liability for its own acts or omissions related to its security responsibilities. Prohibits an airport operator from relieving any qualified private screening company or its employees from any liability related to its own acts of negligence, gross negligence, or intentional wrongdoing.

(Sec. 548) Requires the weekly disaster relief report required by the Second Emergency Supplemental Appropriations Act to Meet Immediate Needs Arising From the Consequences of Hurricane Katrina, 2005 to include specified details on certain allocations, obligations, expenditures, and credit card purchases.