National Fish Hatchery System Act

National Fish Hatchery System Act - Establishes a National Fish Hatchery System (System). Sets forth the objectives of the System, including: (1) mitigating the impacts on fishery resources that result from the construction or operation of Federal projects; (2) restoring certain fish stocks which the Secretary of the Interior (Secretary) determines to be in need of restoration; (3) stocking waters to fulfill international or Indian treaty obligations; (4) carrying out fisheries research and development; and (5) implementing recovery plans for endangered species. Includes as secondary objectives the stocking of Federal waters and waters under the fishery management jurisdiction of Indian tribes if such stocking is not adverse to, or included among, the primary objectives.

Makes a part of such System: (1) Federal agency installations; and (2) non-Federal installations to the extent they are fulfilling System objectives using Federal funding. Excludes moneys made available through specified Federal law from being considered as Federal funding.

Requires the Secretary to administer the System. Requires fish hatcheries not operated by the U.S. Fish and Wildlife Service (Service) to be operated in accordance with a cooperative agreement entered into with the Service. Prohibits fish production within the System four years after enactment of this Act for mitigation or restoration of a fishery resource unless the Secretary completes a mitigation or restoration plan for that resource. Specifies the required content of such plans and the parties to be consulted in formulating the plans.

Permits the production of fish in Federal installations for use by a State in stocking its waters or for private use if System purposes are not hampered or private parties lack private domestic sources.

Authorizes the administering authority to permit, by regulation, the use of a fish research installation, fish health center or fish technology center if the use is compatible with the purposes of the installation. Provides for the enforcement of such regulations.

Provides for the reimbursement of fish production costs from: (1) water or power users benefiting from the mitigation of a Federal water project; (2) Federal agencies or Indian tribes requesting the stocking of waters under their jurisdiction; and (3) State agencies or persons requesting production for non-System objectives. Conditions such fish production upon receipt of such reimbursement.

Requires the Secretary, before October 1, 1986, and within each three year period thereafter, to establish for each System installation the extent to which: (1) the fish production capability of that installation is expected to be utilized; and (2) the primary System objectives will be subject to reimbursement.