The Reagan administration will propose a new customs user fee system that is likely to reduce total importer payments, according to the administration's fiscal 1989 budget.

The new system, which would replace ad valorem fees with a schedule of fixed dollar fees on import entries, would bring in $560 million in federal revenue in fiscal 1989, nearly $140 million less than if the existing system remained in force, the Office of Management and Budget estimates.The administration plans to send the proposed new fee system to Congress shortly, officials say.

The proposal reflects a recent finding by the General Agreement on Tariffs and Trade in Geneva that U.S. assessments of customs fees on the value of imports violate international trade rules.

The existing 0.17 percent customs user fee, the budget office estimates, will bring in $662 million in federal revenue this fiscal year. Basically, the customs user fee, implemented in December 1986, is designed to help defray the Customs Service's processing costs.

The administration meanwhile confirmed that it is asking Congress to continue the Export-Import Bank's lending at about the same level in fiscal 1989 as in the current year.

It proposed a $705 million limit on Ex-Im Bank direct credits next fiscal year, compared with a $690 million ceiling in fiscal 1988. It projected, however, significantly more Ex-Im Bank activity in the issuance of export credit guarantees and insurance both this year and in fiscal 1989.

The administration did not propose an extension beyond this fiscal year of Ex-Im Bank's $210 million war chest to help U.S. exporters counter subsidized foreign export credits. Nor did it propose any measure to bolster the agency's flagging capital base.

The administration's request for funding the Commerce Department's foreign trade-related programs in fiscal 1989 was about the same, overall, as Congress appropriated for fiscal 1988: $169 million.

The department, however, would get more money for both export promotion and export controls as well as for enforcing U.S. laws against unfairly priced imports.

The department's U.S. and Foreign Commercial Service, which helps foster U.S. exports, would receive $91.7 million, up $14 million from this year. Much of the increase is to offset the higher costs of maintaining offices abroad

because of the depreciated dollar.

Commerce, the budget revealed, will propose charging a fee to businesses that use its Commercial Information Management System, an exporter counseling tool.

The department's export control operations would receive $39.6 million in fiscal 1989 under the proposed budget, or nearly $2 million more than allocated this fiscal year. More personnel will be needed to help liberalize export control policy, according to the budget document.

A possible export licensing fee was not included in the budget, but officials said the fee is still under interagency discussion.

The administration proposed to phase out the Commerce Department's adjustment assistance program for U.S. firms hurt by imports. It also indicated that it plans to reduce federal funding for workers left jobless

because of imports or other factors.