Magnuson-Stevens Fishery Conservation and Management Amendments Act of 2006

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.

Requires the Secretary to identify a nation's vessels that have engaged in illegal, unreported, or unregulated fishing (including relevant international fishery management organizations that have failed to implement effective measures to end such activities), or that have engaged in fishing practices beyond the exclusive economic zone that result in bycatch of a protected living marine resource, and to encourage them to take appropriate corrective actions or to enter into bilateral treaties to end such offending activities.