Border Security and Terrorism Prevention Act of 2006

Border Security and Terrorism Prevention Act of 2006 - Directs the Secretary of Homeland Security to: (1) take all appropriate actions, including development of a national border strategy, to maintain operational control over the U.S. international land and maritime borders; (2) report on cross-border security agreements with Mexico and Canada; (3) provide for biometric data enhancements; (4) report on the One Face at the Border Initiative; (5) implement a secure communications plan for Border Patrol and border security use; (6) increase Border Patrol agents, port of entry inspection personnel, and canine detection teams; and (7) report on the airspace security mission's impact on the National Capital Region.

Directs the Secretary to reimburse (up to prior-to-damage value) property owners for costs associated with repairing damages to the property owners' private infrastructure constructed on a U.S. government right-of-way delineating the international land border when such damages are the result of unlawful entry of aliens.

Directs the Secretary to establish at least one Border Patrol unit for the U.S. Virgin Islands by September 30, 2006.

Directs the Secretary to report to the Committee on Homeland Security respecting DHS progress in tracking Central American gangs across the U.S.-Mexico border.

Directs the Secretary to compile specified health care-related data respecting unauthorized aliens taken into U.S. custody.

Directs the Secretary to deploy radiation detection portal monitors at all U.S. ports of entry and facilities within one year of enactment of this Act.

Directs the Secretary: (1) and the Secretary of Defense (DOD) to develop a plan to increase the availability of DOD surveillance equipment along the U.S. international land and maritime borders; (2) to assess border security vulnerabilities on Department of Interior land directly adjacent to the U.S. border; (3) to conduct a border security threat assessment and information sharing exercise; and (4) to establish the Border Security Advisory Committee.

Authorizes the Secretary to permit a state, local government, or Indian tribe to use specified federal funds for border security activities usually performed by a federal agency but which, pursuant to an agreement, are being performed by state, local, or tribal government.

Directs the Secretary to establish a university-based Center for Excellence for Border Security.

Requires mandatory detention of an alien apprehended illegally seeking to enter the United States at a U.S. port of entry or land or maritime border as of October 1, 2006, unless such alien is: (1) paroled into the United States for humanitarian or public benefit reasons; or (2) is permitted to withdraw an application for admission and immediately departs from the United States.

Provides that during the period 60 days after enactment of this Act and prior to October 1, 2006, an apprehended alien may be released with notice to appear only if: (1) the Secretary determines that the alien is not a national security risk; and (2) the alien provides a bond of not less than $5,000.

Directs the Secretary, subject to appropriations, to fully utilize: (1) all Department of Homeland Security (DHS) bed space; and (2) all other options to cost effectively increase detention capacity.

Denies admission to the nationals of a country that refuses or delays acceptance of its nationals ordered removed from the United States.

Directs the Secretary to place an alien (other than from Mexico or Canada) who has not been admitted or paroled into expedited removal if apprehended within 100 miles of the border and within 14 days of unauthorized entry.

Directs the Secretary to take specified actions to ensure coordination of DHS border security efforts.

Establishes in DHS an Office of Air and Marine Operations whose primary mission shall be to prevent the entry of terrorists, other unlawful aliens, instruments of terrorism, narcotics, and other contraband into the United States, and whose secondary mission shall be to assist other agencies with such protective functions.

Directs the Office to operate and maintain the Air and Marine Operations Center in Riverside, California, or other designated facility.

Directs the Secretary to transfer to United States Immigration and Customs Enforcement all functions of the Customs Patrol Officers unit operating on the Tohono O'odham Indian reservation (the "Shadow Wolves" unit). Authorizes the Secretary to establish within United States Immigration and Customs Enforcement additional Customs Patrol units to operate on Indian lands.