Rail Transit Security and Safety Act of 2004

Rail Transit Security and Safety Act of 2004 - Directs the Under Secretary for Border and Transportation Security (Under Secretary) of the Department of Homeland Security (DHS) to complete a vulnerability assessment of freight and passenger rail transportation for identification of: (1) critical assets and infrastructures and threats to them; (2) vulnerabilities specific to the transportation of hazardous materials via railroad; and (3) security weaknesses in passenger and cargo security, transportation infrastructure, protection systems, procedural policies, communications systems, employee training, emergency response planning, and any other area identified by the assessment. Requires the Under Secretary, based on the assessment, to develop specific prioritized recommendations for improving rail security.

Directs the Under Secretary to establish the position of Federal Rail Security Manager within each of at least eight regional areas to: (1) serve as regional coordinator of the Under Secretary's response to terrorist incidents and threats to rail assets; and (2) coordinate efforts related to rail security with State and local law enforcement.

Directs the Comptroller General to study and report to specified congressional committees on the rail passenger transportation security programs in Japan, member nations of the European Union (EU), and other foreign countries in order to identify effective rail transportation security measures.

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

Directs the DHS Secretary to award grants directly to public transportation agencies for allowable capital and operational security improvements.

Establishes a research and development (R&D) program to improve freight and intercity passenger rail security. Directs the Under Secretary to award grants to public or private entities to conduct research into, and demonstration of, technologies to reduce and deter terrorists threats or mitigate damages resulting from terrorist attacks against public transportation systems.

Sets forth certain whistleblower protections for rail employees or other persons who have provided information or otherwise assisted in any investigation regarding certain conduct, or who have refused to violate or assist in the violation of any regulation related to public transportation security.