Customs User Fees Amendments Act of 1989

Customs User Fees Amendments Act of 1989 - Amends the Consolidated Omnibus Budget Reconciliation Act of 1985 to require the Secretary of the Treasury to collect a customs user fee not exceeding $575 for the processing of merchandise that is entered, or withdrawn from warehouse for consumption, during FY 1990.

Requires fees charged for Canadian goods to be in accordance with the U.S.-Canada Free-Trade Agreement. Prohibits such fees from being charged for Israeli products if an exemption is implemented under this Act.

Declares that expenses incurred in conducting commercial operations do not include costs incurred in: (1) air passenger processing; (2) export control; and (3) international affairs. Sets forth certain costs that may not be funded with money contained in the Customs User Fee Account.

Declares that the user fees shall be treated and enforced as if they are customs duties.

Exempts Israeli products from user fees as of the date on which the United States Trade Representative publishes in the Federal Register a determination that Israel has provided reciprocal concessions.

Requires the Comptroller General to report to specified congressional committees on the costs incurred by the U.S. Customs Service in conducting commercial operations and appropriate fees charged to the beneficiaries of such services.

Authorizes the Service to collect user fees for the operation of foreign trade zones at certain small airports that are not ports-of-entry.

Amends the Trade and Tariff Act of 1984 to declare that customs services provided at such a zone shall also be considered provided at such an airport.