National Fishing Fleet Vision, Implementation, and Management Act

Magnuson-Stevens Fishery Conservation and Management Amendments Act of 2006 - Amends the Magnuson-Stevens Fishery Conservation and Management Act (the Act) to authorize appropriations for the national fishery management program through FY2012.

Revises provisions under the Act with respect to: (1) regional fishery management councils; (2) fishery management plan requirements; and (3) environmental review of fishery management plans.

Establishes: (1) limited access privilege programs to harvest fish; (2) Western Pacific regional marine education and training programs; (3) a regional economic transition program for fishermen affected by a catastrophic fishery disaster; (4) a shrimp fisheries hurricane assistance program for the Gulf of Mexico; (5) a bycatch reduction engineering program to minimize bycatch mortality; (6) a community-based fishery and coastal habitat restoration program; and (7) a national fishery permitting and registration program

Increases both civil and criminal penalties for certain prohibited acts under U.S. fishery law. Sets forth a criminal penalty for a person who uses a weapon in the commission of such acts.

National Fishing Fleet Vision, Implementation, and Management Act - Establishes: (1) a National Task Force on Sustainable Fishery Capacity to develop guidance for the development of Sustainable Fishery Vision, Implementation, and Management Plans; (2) a regionally based registry program for recreational fishermen; (3) a cooperative research and management program; (4) a Fisheries Conservation and Management Fund; and (5) a deep sea coral research and technology program.

Reauthorizes certain fisheries Acts through FY2010.