The Air Force recently paid $318 for a C5A aircraft latrine part that should cost less than $100 and ordered seven $5,000 C5A engine mounts for $16,400 apiece, according to the General Accounting Office.

The GAO, the investigative arm of Congress, cited the overpayments in a letter to Defense Secretary Caspar W. Weinberger as evidence that the military's spare-parts problems are not over, despite his initiatives to prevent excessive prices. But the GAO and an aide to Sen. William V. Roth Jr. (R-Del.), who asked for the inquiry, said Weinberger's initiatives have spurred improvements in the spare-parts program.

"This was a kind of heads-up to Mr. Weinberger," one GAO official said. "We noticed a situation that isn't quite right, and we said, 'You folks might want to check around and see if it's occurring anywhere else.' "

A Defense Department spokesman said Weinberger could not comment because he had not seen the letter, but added that the Pentagon is asking other buying centers to make sure there is no pattern of abuse.

"A field-level review at an industrial facility will invariably identify bad buys, as this one has," the spokesman said.

Roth's aide said a wider-ranging investigation is under way and that despite improvements, the Pentagon "obviously still has a ways to go."

"The GAO investigation we requested indicates that they have made some progress, but it also shows that there are a lot of snakes under the rocks out there," the aide said. "The Pentagon is going to get bitten a few more times before they kill all of them."

Among the GAO's findings:

*The Air Force paid $317.97 for "pan toilets" for C5A latrines, which should have cost less than $100 and which were not needed. The pans, weighing about 11 pounds, are thin fiberglass pieces with holes cut in them to fit on the latrine floor. The Air Force decided in 1983 that "the pan was poorly designed" and should no longer be purchased.

A spokesman for Lockheed Corp., prime contractor for the C5A cargo plane and maker of the latrine floor piece, said he could not comment because he had not seen the report.

*The Air Force ordered seven left engine mounts for $16,400 each, after paying less than $5,000 for right-hand mounts. The GAO said the contractor, which other sources identified as Rohr Industries Inc., had agreed to refund about $82,000 for the seven mounts.

But a Rohr spokesman said the arrangement was a "repricing," not a refund, because no money had changed hands when the Air Force requested an adjustment. The spokesman, Jerry Broening, said the $16,400 price had been set in 1982, when the part was no longer in production. Now that parts are being made for the new model C5B, he said, the price could be lowered again.

*The Air Force bought two fiberglass wing panels for the C5A for $5,080 even though identical parts had been in the Air Force's San Antonio warehouse since 1973, the GAO said.

The GAO said the pricing problems on the other parts arose when buyers in San Antonio applied a blanket "rate agreement," which sets acceptable labor and overhead costs, without checking that the formula produced reasonable prices in each case. The buyers made this mistake about one-seventh of the time, the GAO said.

"He the Air Force buyer just looks at the contract and says, 'Sure enough, they're charging us $12 an hour, that's fine,' " the GAO official said.

"But that's no good, because you better also check how many hours they're going to charge you."