Fishing Quota Act of 2003

Fishing Quota Act of 2003 - Amends the Magnuson-Stevens Fishery Conservation and Management Act to require the Regional Fishery Management Councils and the Secretary of Commerce (Secretary) or his designee, when developing a limited access system for fisheries to achieve optimum yield, to take into account: (1) the conservation requirements of this Act with respect to fisheries; and (2) the fair and equitable distribution of a public resource.

Authorizes the establishment of a fishing quota system in a fishery management plan or amendment prepared by any Regional Fishery Management Council or the Secretary.

Specifies fishing quota system: (1) requirements the Councils and Secretary must ensure that any proposal meet; (2) right, tittle, and interest scope and limitations; (3) eligibility requirements; (4) duration; and (5) referendum procedures. Prohibits approval or implementation by the Secretary of any fishery management plan (or amendment) unless it has been approved by more than two-thirds of those voting in a referendum among eligible permit holders.

Authorizes the Secretary to approve and implement a program submitted by a Council which reserves up to 25 percent of the fees collected from fisheries for costs related to the management and enforcement of fishing quota programs for issuance of obligations that aid in financing the: (1) purchase of fishing quotas by small vessel fishermen; and (2) first-time purchase of fishing quotas by entry level fisherman.

Requires the National Research Council to provide an independent review, every five years, of the effectiveness of fishing quota systems conducted in Federal fisheries.

Requires the Secretary to issue regulations which establish requirements for a fishing quota system.