Transportation Security Administration Reorganization Act of 2005

Transportation Security Administration Reorganization Act of 2005 - Amends the Homeland Security Act of 2002 to establish the Airport Screening Organization, headed by the Chief Operating Officer, within the Transportation Security Administration (TSA). Directs the Chief Operating Officer to develop a five-year strategic plan that meets certain performance goals for federal security screening operations for passenger air transportation.

Directs the Assistant Secretary for Homeland Security (TSA) to develop a risk management system to assess and measure potential threats to and from the Nation's transportation system.

Establishes a transportation sector advisory council for each mode of transportation under the TSA jurisdiction.

Amends federal transportation law to replace the security screening opt-out program with the federal security screening partnership program (effectively eliminating the security screening opt-out program where screening of passengers and baggage at airports is contracted out to private screening companies). Directs the Assistant Secretary to develop and update minimum standard operating procedures and requirements for the security screening of passengers in air transportation and interstate air transportation. Directs the Secretary of Homeland Security to issue certificates of conformance to screening entities providing screening services at airports that meet such procedures and requirements.

Requires an operator of an airport to notify the Assistant Secretary of its intention to submit an application under the federal security screening partnership program or to continue to use federal employees in providing screening services for passenger air transportation.

Directs the Assistant Secretary to issue regulations requiring a passenger to present an acceptable personal identification document for inspection before entering a secure area of an airport.

Directs the Secretary to initiate a pilot program to evaluate the use of automated systems for the immediate screening of passengers on international flights to the United States. Requires the Assistant Secretary to submit to Congress a report evaluating the Computer Assisted Passenger Prescreening System (CAPPS).

Sets forth certain training and requalification requirements for federal flight deck officers.