The Defense Department, estimating that escorting reflagged Kuwaiti ships in the Persian Gulf would cost about $200 million a year in extra operating expenses, is preparing to ask Congress to restore millions of dollars cut from its 1988 operations budget request, Pentagon sources said yesterday.

The Pentagon's first request for additional money to support the gulf operations is expected to ignite sharp debate from congressional critics of the Reagan administration's use of U.S. military forces to protect Kuwaiti tankers in the gulf, where Iran and Iraq have been at war for seven years.

Pentagon officials said that by the end of this month the gulf operation, which began in late July, will have cost about $70 million in extra steaming time for ships, flying time for aircraft, danger-pay bonuses for military personnel and additional maintenance requirements.

Pentagon officials say that the extra costs are forcing the Navy to reduce some sea exercises and flight training and defer ship maintenance schedules.

"There are some things in that {operations and maintenance} account which we would have planned to do if we weren't doing this," Deputy Secretary of Defense William H. Taft IV said in an interview this week.

Pentagon sources said that rather than submit a formal supplemental appropriations request, Defense Department officials plan to ask Congress to restore money deleted from their original budget proposal. Congress is still debating the fiscal 1988 budget for the federal government.

House and Senate committees have stripped amounts ranging from $500 million to $900 million from the Navy's $25.6 billion request for operations and maintenance, according to Taft.

"Budget cuts of such a magnitude give us a very bad situation to begin with and the Persian Gulf exacerbates it," another Pentagon official said.

Defense Department officials said there has been disagreement within the Pentagon over the extra costs of the gulf operations. Sources said the Navy estimated the costs would be significantly higher than the $200 million predicted by the Defense Department.

The Navy's proposed budget reportedly included the price of procuring additional equipment for the operations, sources said. The Defense Department deleted those funds, officials said.

None of the budget estimates include the routine costs of operating ships and planes. The Navy has estimated it costs about $1.2 million a day to operate one aircraft carrier group that normally includes a carrier and six to eight support ships.

Already, the Navy has doubled the number of ships assigned to the Persian Gulf and northern Arabian Sea before the escorting missions began. A total of 50 ships and smaller vessels are in the region or have been ordered to the area, including 28 warships, six ocean-going mine-sweepers and six small mine-sweeping vessels, four transport ships and six small speedboats for special operations forces.

In addition, eight Sea Stallion mine-sweeping helicopters are being used in the gulf. Numerous aircraft based on a carrier in the Arabian Sea have been used extensively during the seven convoys thus far.

Any significant additional buildup because of major incidents could exceed the $200 million estimate, sources said.

Pentagon officials say the severe heat and sandstorms of the region have created major maintenance problems for the equipment. As a result, repair and maintenance costs have been significantly higher than when the equipment is used in other areas.