Customs and Trade Facilitation Reauthorization Act of 2006

Customs and Trade Facilitation Reauthorization Act of 2006 - Establishes the Bureau of Customs and Border Protection (CBP) in the Department of Homeland Security (DHS) to replace the U.S. Customs Service in the Department of the Treasury.

Amends the Homeland Security Act of 2002 to replace the Bureau of Border Security with the Bureau of Immigration and Customs Enforcement.

Provides for multilateral customs negotiations.

Requires the Secretary to oversee the establishment of an International Trade Data System.

Amends the Consolidated Omnibus Budget Reconciliation Act of 1985 (COBRA) to extend through FY2010 deposits in, or authorization of appropriations from, the Customs Commercial and Homeland Security Automation Account.

Amends the Tariff Act of 1930 to authorize the Commissioner of Customs (Commissioner) to establish a voluntary government-private sector Customs Industry Partnership Program.

Requires the Commissioner to develop a Trade Resumption Plan in the event of a transportation disruption.

Specifies required components of the Automatic Targeting System for identifying cargo for increased inspection before its clearance in the United States.

Requires the Commissioner to study the feasibility of developing and employing nonintrusive scanning systems in foreign ports.

Establishes within the Bureau of Customs and Border Protection Office of Regulations and Rulings an Intellectual Property Rights Enforcement Division.

Requires the Commissioner to extend the hours of commercial operations at the Santa Teresa Port-of-Entry.

Authorizes appropriations to the U.S. International Trade Commission and the Office of the U.S. Trade Representative.

Requires the Commissioner to establish performance indicators relating to the seizure of methamphetamine and methamphetamine precursor chemicals.

Provides for U.S. port and terminal operator competitiveness.

Amends COBRA to provide for the payment of overtime for CBP employees performing customs border patrol services by charter air carriers for charter flights arriving after normal operating hours.

Amends the Harmonized Tariff Schedule of the United States to consider an article exported and subsequently imported into the United States as retaining its identity notwithstanding that it may contain one or more essential components recovered from other such or similar U.S. exported articles.