Maritime Terminal Security Enhancement Act of 2006 - (Sec. 2) Directs the Commandant of the Coast Guard to require the resubmission of a facility security plan for Coast Guard approval upon the transfer of ownership or operational control over a port terminal facility.
(Sec. 3) Directs the Commandant to require that the individual designated as the Facility Security Officer under a facility security plan be a U.S. citizen.
(Sec. 4) Directs the Secretary of the department in which the Coast Guard is operating (Secretary) to issue regulations by July 1, 2006, that allow access to secure areas within ports and vessels only to maritime workers and merchant mariners who have been issued approved biometric transportation security cards.
(Sec. 5) Directs the Secretary, through the Commandant, to reassess foreign port compliance with international port security requirements and the effectiveness of antiterrorism measures maintained at those ports not less than every five years.
(Sec. 6) Directs the Secretary, by July 1, 2006, to require, and develop the necessary forms and process for, enhanced crewmember identification credentials for U.S. and foreign merchant mariners on vessels that call on U.S. ports.
(Sec. 7) Directs the Secretary to issue implementing regulations for a long range vessel tracking system by April 1, 2007.
(Sec. 8) Directs the Secretary to establish a university-based Center for Excellence for Maritime Domain Awareness.
(Sec. 9) States that a container shipped directly or via a foreign port may enter the United States only if it is: (1) scanned with specified equipment and a copy of the scan is provided to the Commandant; and (2) secured with a specified seal before being loaded on the vessel for shipment.
Directs the Commandant to establish standards for seals and scanning equipment.
Authorizes FY2007-FY2012 appropriations to carry out such container-related activities.
(Sec. 10) Authorizes the Secretary to require the owner or operator of a facility that is required to have a security plan and that is a cargo terminal to submit information, including contracts or other agreements that govern operations of such facilities, to the Secretary to determine if there is any security risk involving such owner or operator.
Directs the Secretary to annually report to Congress regarding contracts and agreements that govern operation of facilities required to have a security plan.