Authorizes the Under Secretary of Homeland Security for Border and Transportation Security (Under Secretary), acting through the TSA, to establish the position of Intermodal Manager throughout regions of the nation to: (1) serve as regional coordinator of the Assistant Secretary of Homeland Security's response to terrorist incidents and threats to maritime and land assets; and (2) coordinate efforts related to maritime and land security with other Department officials, state and local law enforcement, and other public and private entities.

Prohibits the Under Secretary from imposing a passenger security service fee in FY2007 and later unless: (1) such fee is imposed by rule promulgated by the Under Secretary; and (2) Congress approves.

Requires the Assistant Secretary of Homeland Security (TSA) to: (1) report to Congress on the adequacy of training for TSA screeners; and (2) establish an employee internship program for training students to perform screening of passengers and property at airports.

Rail Security Act of 2005 - Directs the Secretary of Homeland Security to establish a task force (including the TSA, the DOT, and other appropriate agencies) to complete a vulnerability and risk assessment of freight and passenger rail transportation. Requires the Secretary, based on the assessment, to develop specific prioritized recommendations for improving rail security.

Authorizes the Secretary of Homeland Security to make grants to Amtrak for certain systemwide security upgrades.

Authorizes the Secretary of Transportation to make grants to Amtrak for certain fire and life-safety improvements and infrastructure upgrades to Amtrak tunnels on the Northeast Corridor.

Authorizes the Secretary of Homeland Security to make grants to freight railroads (including Amtrak), hazardous materials shippers, universities and research centers, and state and local governments for freight and passenger rail security upgrades to prevent or respond to acts of terrorism or sabotage.

Directs the Secretary of Transportation to carry out a research and development (R&D) program to improve freight and intercity passenger rail security.

Directs Amtrak to submit to the National Transportation Safety Board (NTSB) and the Secretary of Transportation a plan to address the needs of families of passengers involved in rail passenger accidents involving an Amtrak intercity train and resulting in a loss of life.

Directs the Secretary of Homeland Security and the Secretary of Transportation to develop and issue guidance for a rail worker security training program to prepare front-line workers for potential threat conditions.

Sets forth certain whistleblower protections for rail employees or other persons who have provided information regarding a perceived threat to security to the employer, Federal Government, or Congress, or who have refused to violate or assist in the violation of any regulation related to rail security.

Directs the Secretary of Homeland Security to require rail carriers transporting high hazardous materials to develop high hazard material security threat mitigation plans containing appropriate measures to address assessed risks to high consequence targets.

Directs the Federal Railroad Administration (FRA) to set forth certain standards for welded rail and tank car safety improvements.

Requires certain rail security studies, including one on the rail passenger transportation security programs in Japan, European Union (EU) member nations, and other foreign countries.

Prohibits a commercial motor vehicle operator registered to operate in Mexico and Canada from operating a commercial motor vehicle transporting a hazardous material in U.S. commerce until the operator has undergone a background records check similar to the background records check required for commercial motor vehicle operators licensed in the United States to transport hazardous materials in commerce.

Sets forth provisions requiring: (1) written route plans for hazardous material motor carriers; (2) the equipping of certain commercial motor vehicles that transport high hazardous materials with wireless terrestrial or satellite communications technology; (3) the review of hazardous materials security plans of shippers or carriers of hazardous materials; (4) the development of a Pipeline Security and Incident Recovery Protocols Plan; (5) the review of pipeline operator adoption of certain recommendations, including pipeline security plans and critical facility inspections; and (6) the development of a national public sector response system to respond to accidents, threats, and other safety and security risks or incidents.

Directs the Assistant Secretary of Homeland Security to make grants to private operators of over-the-road buses for certain system-wide security improvements to their operations.

Directs the Secretary of Homeland Security to establish joint operational centers for port security at all Tier 1 ports in order to improve interagency cooperation and sharing of intelligence information so as to provide greater protection for port and intermodal transportation systems against terrorism.

Amends federal shipping law to require the Administrator of the Maritime Administration to identify foreign assistance programs that could facilitate implementation of port security antiterrorism measures in foreign countries. Requires importers shipping goods to the United States via cargo container to supply entry data under an advance notification system. Increases the number of overseas U.S. Customs Service inspectors for inspecting intermodal shipping containers being shipped to the United states. Calls for random inspection of shipping containers.

Requires the promulgation of standards and procedures for the inspection and screening of cargo in foreign ports intended for shipment to the United States.

Directs the Secretary of Homeland Security to promulgate a strategic plan for transportation R&D.

Amends the Homeland Security Act of 2002 to establish within the Directorate of Science and Technology of the Department of Homeland Security a competitive research program that supports projects related to homeland security research.

(Sec. 103) Amends federal shipping law to require a minimum authorization of appropriations of $35 million for each of FY2005-FY2009 for implementation of new technology projects to improve port security. (Current law authorizes appropriations of $35 million for each of FY2005-FY2009.)

Directs the Secretary of Homeland Security (Secretary) to set-aside specified percentages of TSA and the Directorate of Science and Technology research and development (R&D) funds for: (1) maritime security related projects or programs, including ferry systems (8%); and (2) rail security related projects or programs (2%).

Directs the Secretary to promulgate a strategic plan for transportation R&D that ensures that the research needs for security of all modes of transportation, including aviation, maritime, rail, pipeline, and transit security, are addressed. Requires the Homeland Security Science and Technology Advisory Committee to annually evaluate the plan, and recommend changes to the transportation security research program under such plan. Requires the Secretary to report to Congress on such plan, including the evaluations and recommendations made by the Advisory Committee.

Authorizes the Secretary to transfer up to $15 million each fiscal year to the National Institute of Science and Technology (NIST) for a focused program in transportation security under its Advanced Technology Program.

Amends the Homeland Security Act of 2002 to direct the Secretary, acting through the Under Secretary for Science and Technology (Directorate of Science and Technology for the Department of Homeland Security (DHS)) (Under Secretary), to establish a competitive research program, headed by a Director, within the Directorate. Requires the Director to provide assistance to certain institutions of higher education for R&D projects that are related to, or qualify as, homeland security research. Sets forth program funding requirements.

(Sec. 104) Requires the Secretary to notify Congress not less than 15 days before any DHS reorganizations.

(Sec. 105) Amends federal transportation law to eliminate a provision requiring the application of the Federal Aviation Administration's (FAA) acquisition management system to acquisitions of equipment, supplies, and materials made by the TSA.

Title II: Improved Aviation Security - (Sec. 201) Prohibits the Assistant Secretary of Homeland Security (TSA) (Assistant Secretary) from increasing an aviation security infrastructure fee imposed on air carriers, or imposing any additional air carrier fees, in FY2007 and later unless: (1) such fee or increase is imposed by rule promulgated by the Assistant Secretary; and (2) the rule is submitted to specified congressional committees.

(Sec. 202) Requires the Assistant Secretary to: (1) conduct a study, and report the results to Congress, on the feasibility of collecting the passenger security service fee directly from passengers at, or before they reach, the airport through a system developed or approved by the Assistant Secretary, including the use of vending kiosks, other automated vending devices, the Internet, or other remote vending sites; and (2) develop, based on such study, feasible and efficient alternative collection systems. Directs the Assistant Secretary to conduct demonstration projects at small, medium, and large hub airports if the Assistant Secretary determines that a system of direct collection of passenger fees at airports is feasible.

(Sec. 203) Requires the Assistant Secretary to establish an employee internship program for training students to perform screening of passengers and property at airports.

(Sec. 204) Prohibits the Administrator of the FAA from certifying foreign aircraft repair stations if final regulations ensuring the security of such foreign (including domestic) repair stations have not been issued within 90 days of enactment of this Act.

Title III: Improved Rail Security - Rail Security Act of 2005 - (Sec. 302) Directs the Secretary to establish a task force (including the TSA, the DOT, and other appropriate agencies) to complete a vulnerability and risk assessment of freight and passenger rail transportation. Requires the Secretary, based on the assessment, to develop specific prioritized recommendations for improving rail security. Requires the development of plans for: (1) the federal government to provide increased security support for freight and intercity passenger railroads at high threat level alert; (2) coordinating existing and planned rail security initiatives undertaken by the public and private sectors; and (3) the continued movement of freight and passengers in the event of an attack against the railroad system. Requires the Secretary to submit to Congress a report containing the assessment, prioritized recommendations, and plans, including an estimate of the cost to implement such recommendations. Authorizes funding for FY2007.

(Sec. 303) Authorizes the Secretary to make grants to the National Railroad Passenger Corporation (Amtrak) for certain systemwide security upgrades. Requires that the award of such grants be for projects contained in an approved systemwide security plan that includes measures to address security awareness, emergency response, and passenger evacuation training. Makes funds available for FY2007-FY2009.

(Sec. 304) Authorizes the Secretary of Transportation to make grants to Amtrak for certain fire and life-safety improvements and infrastructure upgrades to Amtrak tunnels on the Northeast Corridor in New York, NY, Baltimore, MD, and Washington, DC. Authorizes appropriations for FY2007-FY2009. Earmarks an amount for FY2007 for the preliminary design of options for a new tunnel on a different alignment to augment the capacity of the existing Baltimore tunnels. Prohibits the Secretary of Transportation from making funds available to Amtrak for such upgrades until Amtrak has submitted, and the Secretary of Transportation has approved, an engineering and financial plan and a project management plan.

(Sec. 305) Authorizes the Secretary to make grants to freight railroads (including the Alaska Railroad and Amtrak), hazardous materials shippers, universities and research centers, and state and local governments for certain freight and passenger rail security upgrades to prevent or respond to acts of terrorism or sabotage. Requires that the award of such grants be for projects contained in an approved systemwide security plan that includes measures to address security awareness, emergency response, and passenger evacuation training. Sets forth prioritized allocation requirements, limiting the award of grants for rail security upgrades to no more than $45 million to Amtrak, or no more than $80 million for the transportation of hazardous materials by rail. Authorizes appropriations for FY2007-FY2009.

(Sec. 306) Directs the Secretary, through the Under Secretary and the Assistant Secretary, to carry out a R&D program to improve freight and intercity passenger rail security. Requires the Secretary to coordinate the R&D program with other R&D initiatives at the DHS and DOT. Authorizes appropriations for FY2007-FY2009.

(Sec. 307) Authorizes the Secretary to use 0.5% of funds for Rail Security Act of 2005 capital projects for oversight of such projects. Directs the Secretary to prescribe procedures and schedules for the award of grants under the Rail Security Act of 2005.

(Sec. 308) Directs Amtrak to submit to the National Transportation Safety Board (NTSB), the Secretary of Transportation, and the Secretary a plan to address the needs of families of passengers involved in rail passenger accidents involving an Amtrak intercity train and resulting in a loss of life. Limits Amtrak's liability for damages in any action brought in a federal or state court arising out of its performance in preparing or providing a passenger list, or in providing information concerning a train reservation, unless such liability is caused by Amtrak's conduct. Earmarks amounts to Amtrak for FY2007 to carry out this section.

(Sec. 309) Directs the Secretary, the Secretary of Transportation, heads of other appropriate federal departments and agencies, and Amtrak to report to Congress on the current system for preclearance and screening of rail and airline passengers and baggage, as well as freight railroad traffic, between the United States and Canada, including progress on a rail passenger preclearance protocol.

(Sec. 310) Directs the Secretary and the Secretary of Transportation to develop and issue guidance for a rail worker security training program to prepare front-line workers for potential threat conditions. Requires rail carriers to: (1) develop a rail worker security training program based on such guidance and submit it for review by the Secretary; and (2) not later than one year after such review, complete the training of all front-line workers.

(Sec. 311) Sets forth certain whistleblower protections for rail employees or other persons who have provided information regarding a reasonably perceived threat to security to the employer, federal government, or Congress, or who have refused to violate or assist in the violation of any regulation related to rail security.

(Sec. 312) Directs the Secretary to require rail carriers transporting high hazardous materials to develop high hazard material security threat mitigation plans containing appropriate measures (including alternative routing and temporary shipment suspension options) to address assessed risks to high consequence targets. Requires rail carriers that transport high hazardous materials on a right-of-way to institute such plans when the threat levels of the Homeland Security Advisory System are high or severe and specific intelligence of probable or imminent threat exists as to a high-consequence target being within the catastrophic impact zone of the railroad right-of-way used to transport high hazardous material, or rail infrastructure or operations being within the immediate vicinity of such target.

(Sec. 313) Directs the Secretary of Transportation and the Secretary to execute and develop an annex to the memorandum of agreement between the DOT and DHS signed on September 28, 2004, governing the roles, responsibilities, resources and commitments of the two departments in addressing railroad transportation security matters.

(Sec. 314) Directs the Secretary of Transportation to review existing DOT rail regulations to identify areas needed to be revised to improve rail security.

(Sec. 315) Directs the Secretary to develop a national plan for public outreach to increase awareness of measures that the general public, railroad passengers, and railroad employees can take to increase railroad system security.

(Sec. 316) Directs the Secretary to to develop a program to encourage the equipping of rail cars transporting high hazard materials with wireless terrestrial or satellite communications technology. Earmarks certain funds for FY2007-FY2009 to carry out this section.

Title IV - Improved Motor Carrier, Bus, and Hazardous Material Security - (Sec. 401) Requires motor carriers that are required to have hazardous material safety permits to operate in transporting hazardous materials to maintain written route plans that meet certain requirements.

(Sec. 402) Requires the Secretary to develop a program to encourage the equipping of motor carriers transporting high hazard materials with wireless communications technology. Earmarks certain funds for FY2007-FY2009 to carry out this section.

(Sec. 403) Directs the Secretary to develop and make available in written or electronic form security training guidelines for short-term truck leasing operations consistent with existing best practices as determined by the Secretary.

(Sec. 404) Establishes within the TSA a program for reviewing hazardous materials security plans of shippers or carriers of hazardous materials. Sets forth civil penalties for failure of a shipper, carrier, or other person to comply with certain requirements for the transportation of hazardous materials.

Requires the Secretary to study the extent insurance, security, and safety costs borne by railroad carriers, motor carriers, pipeline carriers, air carriers, and maritime carriers associated with the transportation of hazardous materials are reflected in rates paid by shippers of such commodities as compared to the costs and rates respectively for the transportation of non-hazardous materials. Earmarks certain funds for FY2007-FY2009 to carry out this section.

(Sec. 405) Requires the Secretary of Transportation to submit to Congress a report assessing truck security.

(Sec. 406) Directs the Secretary to develop a Pipeline Security and Incident Recovery Protocols Plan that includes: (1) the federal government providing increased security support to critical interstate and intrastate natural gas and hazardous liquid transmission pipeline infrastructure and operations during high or severe security threat levels of alert; and (2) incident recovery protocols to ensure continued transportation of natural gas and hazardous liquids in the event of an incident. Requires the Secretary to report to Congress on such plan. Earmarks certain funds for FY2007 to carry out this section.

(Sec. 407) Establishes a program to review pipeline operator adoption of certain federal pipeline recommendations, including the review of pipeline security plans and an inspection of certain critical pipeline facilities. Requires the Secretary in reviewing pipeline compliance to utilize risk assessment methodologies to prioritize vulnerabilities and to target inspection and enforcement actions to the most vulnerable and critical pipeline assets. Earmarks certain funds for FY2007 and FY2008 to carry out this section.

(Sec. 408) Directs the Secretary of Transportation and the Secretary to execute and develop an annex to the memorandum of agreement between the DOT and DHS signed on September 28, 2004, governing the roles, responsibilities, resources and commitments of the two departments in addressing pipeline security and hazardous materials transportation security matters.

(Sec. 409) Directs the Secretary, in conjunction with the Secretary of Transportation, to develop a national public sector response system to respond to accidents, threats, and other safety and security risks or incidents. Requires the Secretary to report to Congress on the costs to establish such system. Earmarks certain funds for FY2007-FY2009 to carry out this section.

(Sec. 410) Directs the Secretary to make grants to private operators of over-the-road buses or over-the-road-bus terminal operators for certain system-wide security improvements to their operations. Prohibits the Secretary from making a grant to a private operator of over-the-road buses until the operator submits to the Secretary a plan for making the security improvements. Requires the Secretary to submit to Congress an assessment of the over-the-road bus security grant program. Earmarks certain funds for FY2007-FY2009 to carry out this section.

Title V: Improved Maritime Security - (Sec. 501) Directs the Secretary to establish interagency operational centers for port security at all high priority ports (Miami, Florida, Norfolk/Hampton Roads, Virginia, Charleston, South Carolina, and San Diego, California) in order to improve interagency cooperation and sharing of intelligence information so as to provide greater protection for port and intermodal transportation systems against terrorism.

(Sec. 502) Amends federal shipping law to require area maritime transportation security plans to include, among other things, a salvage response plan that: (1) identifies salvage equipment capable of restoring operational trade capacity; and (2) ensures that the flow of cargo through U.S. ports is re-established quickly as possible after a transportation security incident.

(Sec. 503) Revises provisions requiring the National Maritime Transportation Security Plan to include a plan for ensuring that the flow of cargo through U.S. ports is reestablished as efficiently and quickly as possible after a transportation security incident to also provide, to the extent practicable, preference in the reestablishment of the flow of cargo to vessels: (1) that have a vessel security plan; (2) that are manned by crewmembers who have undergone a background check or who hold transportation security cards; and (3) on which all cargo has undergone inspection.

(Sec. 504) Directs the Secretary of the department in which the Coast Guard is operating to identify foreign assistance programs that could facilitate implementation of port security antiterrorism measures in foreign countries. Requires the Secretary of the department in which the Coast Guard is operating to establish a program to utilize those programs that facilitate implementation of port security antiterrorism measures at foreign ports that lack effective antiterrorism measures, with particular emphasis at ports located in the Caribbean Basin.

Directs the Secretary of State to negotiate with foreign governments and certain international organizations to promote international security standards for containers and other cargo moving within the international supply chain and to encourage compliance with minimum technical requirements for non-intrusive inspection equipment, including imaging and radiation detection devices.

Directs the Comptroller General to report to Congress on the security of ports in the Caribbean Basin, including an assessment of the effectiveness of the measures employed to improve security at such ports.

(Sec. 505) Requires importers shipping goods to the United States via cargo container to supply entry data under an advance notification system so as to provide the best possible data for the U.S. Customs and Border Protection's automated targeting system that identifies high-risk cargo for inspection before it is loaded in a foreign port for shipment to the United States. Authorizes appropriations for FY2007-FY2009.

(Sec. 506) Directs the Commissioner of Customs and Border Protection (Commissioner) to initiate a rulemaking to establish minimum technical requirements for non-intrusive inspection equipment, including imaging and radiation detection devices, that help ensure that all equipment used can detect risks and threats as determined by the Secretary of the department in which the Coast Guard is operating.

(Sec. 507) Requires the Commissioner to develop and implement a plan for random physical inspection of shipping containers in addition to any targeted or pre-shipment inspection of such containers.

(Sec. 508) Directs the the Secretary of the department in which the Coast Guard is operating, through the Commissioner, to issue regulations to: (1) evaluate and screen cargo documents prior to loading in a foreign port for shipment to the United States; and (2) physically or by nonintrusive technology inspect high-risk cargo in a foreign port intended for shipment to the United States. Directs the Commissioner to execute inspection and screening protocols with authorities in foreign ports to ensure that such regulations are effectively implemented. Authorizes appropriations for FY2007-FY2009.

(Sec. 509) Revises elements under the secure systems of international intermodal transportation program, including requiring the establishment of standards and procedures for verifying that a container at the point at which goods are placed in the container for shipping is free of unauthorized hazardous chemical, biological, or nuclear material. Authorizes the Commissioner to provide expedited clearance of cargo to an entity that meets or exceeds the standards and procedures and certifies the security of its supply chain not less than once every two years.

(Sec. 510) Directs the Secretary to conduct, and submit to Congress, a port security user fee study.

(Sec. 511) Requires the Secretary of the department in which the Coast Guard is operating to issue a final rule requiring the issuance of transportation security cards to individuals who enter secure areas of a vessel or maritime facility.

(Sec. 512) Requires the Secretary of the department in which the Coast Guard is operating to establish a grant program based on risk and vulnerability (currently, for making a fair and equitable allocation of funds) to implement Area Maritime Transportation Security Plans and facility security plans among port authorities, facility operators, and state and local government agencies required to provide port security services.

(Sec. 513) Directs the Secretary, through the Commissioner, to issue regulations to: (1) strengthen the validation process in verifying that security programs of Customs-Trade Partnership Against Terrorism members have been implemented; and (2) implement a records management system. Requires the Secretary of the department in which the Coast Guard is operating to complete a human capital plan that describes how the Customs-Trade Partnership Against Terrorism program will recruit, train, and retain staff, including reviewing security profiles, vetting, and conducting validations to mitigate program risk. Authorizes appropriations for FY2007-FY2009.

(Sec. 514) Provides that economic disruption in a particular area in defining what is a transportation security incident shall not include a work stoppage or other non-violent employee-related action resulting from an employee-employer dispute.

(Sec. 515) Establishes an appeal process for individuals who have been found ineligible and denied a waiver for the issuance of a transportation security card.

(Sec. 516) Directs the Secretary, acting through the Commissioner, in coordination with the Secretary of State, and their Canadian counterparts, to develop a plan for the inspection of passengers and vehicles before they board, or are loaded onto, a ferry bound for a U.S. port.