National Wildlife Refuge System Act of 1990

National Wildlife Refuge System Act of 1990 - Amends the National Wildlife Refuge System Administration Act of 1966 to require the Secretary of the Interior, acting through the Director of the U.S. Fish and Wildlife Service, to issue regulations governing the manner of finding whether an existing or proposed new use in a refuge is compatible or incompatible with the established purposes of such refuge.

Directs the Secretary to prepare and revise at least once every ten years a comprehensive plan governing the administration of the National Wildlife Refuge System.

Requires the Director to: (1) review, within two years of enactment of this Act, cooperative agreements and memoranda of understanding governing refuges not under the primary jurisdiction of the Service; and (2) negotiate modification of terms and conditions with the appropriate agencies, if needed, to achieve the purposes for which the refuges were established.

Directs the Secretary to identify and discontinue incompatible and harmful uses of refuges that do not meet established refuge purposes.

Requires annual reports to specified congressional committees, together with one special report, a year after enactment, on: (1) the usefulness of comprehensive planning for individual refuges; (2) the extent to which inappropriate uses have occurred on refuges because of insufficiently clear or comprehensible purposes; and (3) the role of the System in maintaining biological diversity in the United States.