Rail and Public Transportation Security Act of 2006 - Amends the Homeland Security Act of 2002 to direct the Secretary of Homeland Security (Secretary) for the Department of Homeland Security (DHS) to develop and implement, and update as appropriate, a National Rail and Public Transportation Security Plan.
Requires the Secretary, acting through the Transportation Security Administration (TSA), to promulgate regulations that require a railroad carrier or public transportation system owner or operator to: (1) conduct an assessment of the vulnerability of the rail or public transportation system to terrorism; and (2) prepare and implement a security plan that addresses identified vulnerabilities.
Directs the Secretary to develop, and submit to Congress, a Rail and Public Transportation Strategic Information Sharing Plan.
Establishes a grant program to allocate federal assistance to U.S. rail and public transportation systems. Sets forth uses of such grants, including to remedy rail and public transportation security vulnerabilities identified in the assessments.
Requires rail and public transportation systems to develop for its workers a rail and public transportation security training program that conforms to guidelines established by the Secretary.
Establishes: (1) a Rail and Public Transportation Security Exercise Program; and (2) a research and development program to improve rail and mass transit security.
Sets forth certain whistleblower protections for DHS and rail employees (including federal contractors and subcontractors) 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 national or homeland security.
Requires an increase in the number of DHS rail security inspectors.