WASHINGTON (AP) _ The lid has been lifted off another expensive parts purchase by the Pentagon, which has acknowledged paying more than $600 for a plastic and fiberglass cover for toilets on its P-3 submarine-hunting airplanes.

One senator said the discovery ''gives new meaning to the word 'throne.'''

The Pentagon, acknowledging the purchases on Monday, said it wasn't sure how much the covers should cost, ''but we obviously feel this is too much,'' spokesman William Caldwell said.

The primary contractor of the plane, the Lockheed Corp., said it charged an average of $640.09 each for the covers. But the company says it has determined that the correct price is $554.78 each. The company notified the Navy that it was prepared to refund the difference, a total of $4,606.74, Lockheed spokesman Jim Ragsdale said.

But a Defense Department official, who spoke only on condition of anonymity, said the Pentagon had not accepted Lockheed's refund offer. ''That's what they've offered, but we haven't determined they're offering enough.''

Questions about expensive toilet seats on the P-3 were raised during a Senate Armed Services Committee hearing by Sen. William S. Cohen, R-Maine, who said the pricetag ''gives new meaning to the word, 'throne.'''

In a statement Monday, the Pentagon said the senator was wrong in referring to a ''toilet seat.'' The statement said, however, Cohen was probably referring to ''a lavatory cover which we have recently learned has been priced at more than $600 by the contractor, Lockheed Corp.''

''As soon as the high cost of this item was brought to our attention, we issued a stop order to prevent further purchases and directed that the item go out for competitive bid,'' the Pentagon added.

The Defense Department has been under fire for expensive parts purchases, prompted by stories about such things as a $7,600 coffeemaker for the C-5 transport and a plastic cap for an airplane stool listed at more than $1,000.

Caldwell and Lockheed described the toilet cover as a special piece of molded plastic and fiberglass that fits over the frame of the airplane's toilet and provides the anchor to which the toilet seat is bolted. The toilet seat itself costs $10.80, Caldwell said.

The P-3 Orion is a four-engine turboprop patrol plane designed to fly for hours at a time while it hunts and destroys enemy submarines. There are 429 of the planes in the Navy's inventory, and the fiscal 1986 budget calls for buying nine more.