Sen. William S. Cohen (R-Maine) charged yesterday that the Navy has been paying more than $600 each for toilet seats, which he said "gives new meaning to the word 'throne.' "

The Navy calls the item a "toilet cover assembly," and Lockheed-California Co. concluded after a recent review that it was only modestly overpriced.

Lockheed, which makes the plastic-and-fiberglass cases for toilets on P3 Orion submarine-hunting planes, said the housings should cost $554.78, not the $640.09 it had charged.

As a result, Lockheed recently refunded the Navy $4,606.74.

Pentagon spokesman William Caldwell said the Defense Department does not know how much the toilet parts should cost, "but we obviously feel this is too much."

He said Pentagon engineers are studying the part.

The overcharging came to light when the Pentagon put the part out for competitive bid, he said.

Last October, Navy officials said the service paid $16,571 for a three-cubic-foot refrigerator designed to hold crew lunches and drinks during long flights on the P3.

An aide to Sen. William V. Roth Jr. (R-Del.), who has been investigating the toilet matter, said that the Pentagon included the most recent Lockheed price in its request for new bids, which he said might discourage lower bids.

The aide said several manufacturers have said they could make the part for less.

But a Lockheed spokesman, Jim Ragsdale, said the price reflects the fact that the Navy orders only a few of the parts at a time -- 54 in 1984.

"If the Navy had needed 54,000 of them, I'm sure the price . . . would have been substantially less," he said.

"What I don't understand about this procurement is why we have an aircraft manufacturer making toilet covers," Roth said.

"Would we ask a toilet company to build a C5?"