Fishery Conservation and Management Amendments Act of 2004

Fishery Conservation and Management Amendments Act of 2004 - Amends the Magnuson-Stevenson Fishery Conservation and Management Act to: (1) extend, through FY 2008, the authorization of appropriations under the Act; (2) provide for implementation of a treaty between the United States and Canada concerning Pacific coast albacore tuna fishing; and (3) allow, with respect to Pacific insular area fisheries and fishing agreements, monitoring programs that the Secretary of Commerce determines to monitor harvests by foreign fishing vessels.

Requires fishery management plans (plans) for Federal fisheries to include harvest and processing revenues, production costs, capital expenditures, and other fishing or processing expenses. Allows any plan established by a regional fishery management council to establish a fishing quota system for achieving optimum yield, including compliance with specified quota share and allocation requirements. Requires: (1) a quota system to be approved in advance by more than two-thirds of those voting in a referendum among eligible fishing permit holders; (2) the National Research Council, every five years, to provide an independent review of the effectiveness of fishing quota systems in Federal fisheries; and (3) the Secretary to issue regulations establishing requirements for the quota system. Directs the Secretary to: (1) make a preliminary evaluation of a plan or amendment, or a regulation concerning a plan or amendment; and (2) take specified action, depending on whether evaluation results are positive or negative.

Directs the Secretary to promulgate regulations governing fishing after January 1, 2008, that: (1) limit fishing mortality to specified rates; and (2) allocate both fishing restrictions and recovery benefits fairly among fishery gear sectors and communities.

Authorizes the Secretary to: (1) conduct a fishing capacity reduction program in a fishery under the authority of the Secretary, a regional council, or a State; and (2) implement an information collection or observer program for the collection of necessary additional information under a plan. Allows plan information to be disclosed to State employees responsible for plan monitoring.

Directs the Secretary to establish a national cooperative research and management program between fishing industry participants, affected States, and the National Marine Fisheries Service (Service). Requires an independent review of the Service's procedures for ensuring data quality in the data collection phase of the stock assessment program.

Authorizes Federal-State cooperative marine law enforcement agreements.

Requires the Scientific and Statistical Committees of each council to identify and report to the Secretary priority research needs to support ecosystem-based management of fisheries within its jurisdiction.