9/11 Commission Recommendations Implementation Act of 2006

9/11 Commission Recommendations Implementation Act of 2006 - Authorizes appropriations, including for: (1) FY2007 for the Edward Byrne Memorial Justice Assistance Grant Program and the Office of Community Oriented Policing Services; (2) FY2007-FY2017 for the State Homeland Security Grant Program, the Urban Area Security Initiative Grant Program, and the Law Enforcement Terrorism Prevention Program; and (3) FY2007-FY20011 for the addition of more Federal Bureau of Investigation (FBI) agents, grants for interoperable communications technology, Northeast Corridor fire and life-safety improvements, and consolidation of terrorist watch lists. Requires a review and update of the national response plan to coordinate a state and local response within eight to 24 hours after a natural disaster or terrorist attack.

Requires: (1) a critical infrastructure vulnerability assessment, including comprehensive threat reduction recommendations for each critical area; and (2) a vulnerability assessment of freight and passenger rail transportation, including a northern border rail report and development of specific prioritized recommendations for improving rail security.

Requires the issuance of regulations that establish a national, risk-based policy for extremely hazardous materials transported by rail or being stored. Sets forth transportation related whistleblower protection provisions.

Authorizes appropriations for FY2007-FY2011 for: (1) grants for improving the security of chemical plants and ports; and (2) screening of all checked passenger luggage and cargo on commercial flights.