Project SeaHawk Implementation Act of 2006 - Directs the Secretary of Homeland Security, acting through the Commandant of the Coast Guard, to establish or designate an interagency operational center for maritime and port security in each region designated by the Commandant as a Coast Guard sector. Declares that the purpose of each center is to facilitate day-to-day operational coordination, interagency cooperation, unity of command, and the sharing of intelligence information in a common mission to provide greater protection for port and intermodal transportation systems against acts of terrorism. Sets forth certain center requirements, including that each center be modeled on the Charleston Harbor Operations Center (popularly known as Project SeaHawk) administered by the U.S. Attorney's Office for the District of South Carolina for the Port of Charleston located in Charleston, South Carolina.
Requires the head of each center to: (1) assist in implementation of maritime transportation security plans and transportation security incident response plans; (2) conduct short- and long-range vessel tracking and other maritime intelligence activities; and (3) be incorporated into the screening and high-risk cargo inspection programs carried out by the Bureau of Customs and Border Protection.