Public Transportation Security Assistance Act of 2006

Public Transportation Security Assistance Act of 2006 - Title I: Public Transportation Security - (Sec. 101) States that the purpose of this title is to provide grants to public transportation agencies and over-the-road bus operators to improve security in a manner consistent with the recommendations of the National Commission on Terrorist Attacks Upon the United States (9/11 Commission).

(Sec. 103) Requires the Secretary of Transportation (Secretary) to request the Secretary of Homeland Security take action to ensure that a security assessment is made of each public transportation system. Requires each public transportation agency that receives an assessment to develop a prioritized plan of needed capital and operational security improvements.

(Sec. 104) Requires the Secretary to make grants to eligible public transportation agencies for certain capital security improvements and operational security improvements. Sets the federal share of such security project costs at 80% and 50%, respectively. Requires the Secretary of Homeland Security to allocate grants based on the results of the security assessment and in a manner that prioritizes such grants each fiscal year based on risk, consequences, vulnerability, and threat.

Directs the Secretary to establish security improvement priorities for each public transportation agency receiving a security assessment. Requires each public transportation agency to: (1) identify a security coordinator to coordinate security improvements; (2) develop a comprehensive plan that demonstrates the agency's capacity to operate and maintain purchased security equipment; and (3) report annually to the Department of Transportation (DOT) on the use of grant funds.

(Sec. 105) Requires the Secretary to request that the Secretary of Homeland Security provide notification of all credible terrorist threats against public transportation assets in the United States. Requires the Secretary to fund the reasonable costs of the Information Sharing and Analysis Center for Public Transportation (ISAC) established pursuant to Presidential Directive 63 to protect critical infrastructure. Requires public transportation agencies that are at significant risk of terrorist attack to participate in the ISAC.

(Sec. 106) Directs the Secretary to report to Congress on implementation of security measures instituted in this Act.

(Sec. 107) Directs the Secretary to develop and issue guidelines for a public transportation employee security training program. Requires a public transportation agency that receives a public transportation security assessment to develop, and submit for the Secretary's approval, an employee training program in accordance with such guidelines.

(Sec. 108) Authorizes appropriations for FY2007-FY2009 for: (1) capital security improvements and operational security improvements; and (2) the ISAC.

Title II: Over-The-Road Bus Security Assistance - (Sec. 201) Directs the Secretary to establish a program to make grants to private operators of over-the-road buses for certain system-wide security improvements to their operations. Sets the federal share of security project costs at 80%.

Directs the Administrator of the Federal Motor Carrier Safety Administration to conduct, and report to the Secretary and the Secretary of Homeland Security on, a study of the critical systems of the nationwide over-the-road bus industry, including security threats and security weaknesses in such systems, and backup systems required to continue operation of the systems in the event of a terrorist attack or other incident. Requires the Secretary to allocate grants according to certain established priorities based on the report.

(Sec. 202) Prohibits the Secretary from making a grant to a private operator of over-the-road buses until the operator submits to the Secretary: (1) a plan for making security improvements that has been approved by the Secretary; and (2) such additional information as the Secretary may require to ensure accountability for the obligation of grant amounts.

(Sec. 204) Directs the Secretary to submit to Congress a preliminary report that includes an assessment of the over-the-road bus security grant program. Authorizes appropriations for FY2007-FY2009.