The General Accounting Office and the Pentagon are locked in a bitter top-secret fight about whether radar fuzes on the nation's newest family of strategic missile warheads can be jammed, causing them to explose prematurely or not at all.

The congressional investigators, in a highly classified report, charge that the new Mark 12A warheads for the land-based Minuteman III intercontinental ballistic missile (ICBM) are vulnerable to jamming. That finding has "raised doubts about the future overall effectiveness of strategic forces," according to a GAO source.

However, a top Pentagon official involved in missile development yesterday called the GAO study "a red herring and annoyance" that "in a technical sense is correct" but "misunderstands how the warhead systems operate."

Prefacing his next remark by saying "this is extremely sensitive" since the fuzing system "is the guts of the weapons," the Pentagon official said the GAO investigators did not recognize that the radar fuze "has systems to back it up."

The GAO's report grows out of its 1978 investigation of the Mark 12A warhead, which will make the Minuteman III the most powerfull weapon in the U.S. strategic arsenal.

The Mark 12A carries three separete hydrogen bombs, called reentry vehicles or RVs in weapon-maker language.

Each RV houses a tiny radar set which constantly measures the distance to the ground by sending out an electronic pulse and recording how long it takes to bounce back.

When the radar records the correct altitude, it closes the fuze, beginning the firing process that culminates in the hydrogen explosion.

On earlier model ICBM warheads, the final fuzing was done by a pressure-measuring device that is less precise than the new radar in determining altitudes.

The GAO report argues that the Soviet Union could deploy radar search and jamming equipment to foil in incoming RV radars.

A top nongovernment scientist associated with building strategic missile warheads said doubts raised by the GAO are "misdirected."

"On the surface it is very alarming," he said, "but how serious is it in a realistic sense?"

He doubts the Soviets would go to the expense of building extensive radar-jamming equipment.

If they did, however, "we would go with our backup fuzes although that would leave the warhead not quite as accurate."

He also said he doubted the Soviet search radar could successfully send out false signals that would make any incoming U. S. warheads explode prematurely. He conceded that they could use such signals to make the radar inoperative.

The GAO first presented its findings on the Mark 12A radar vulnerability to the Pentagon last summer. At that time, a GAO source said, Defense Department officials "admitted the problem exists" and made provision to do something about it.

A Pentagon official yesterday recalled it differently.

The GAO "thought they had uncovered something important and wanted us to turn things inside out in a crash effort," he said.

He conceded that the Pentagon did "a reassessment" of vulnerabilities of the Mark 12A, but said nothing new came of it. "One new idea is being pursued in advanced research" for the next generation of warheads, he added.

The GAO, he said, "did feel hurt when we didn't change fuzes. Now they are out to put pressure on us."

The GAO has given a griefing on the fuze problem to the House Armed Services subcommittee on research and development. A GAO source described the members as "quite shocked."

A Pentagon official said the under secretary for research and engineering, William J. Perry, and his chief deputy for strategic systems, Seymour L. Zeiberg, briefed the subcommittee and "now everyone's happy."

No subcommittee member was willing to comment on the matter. However, it was learned that the members generally believe that the GAO may be overstating the case and that the Pentagon may be understating the lawmakers' concern. The subcommittee reportedly has asked the Pentagon officials to gather additional information on the disagreement.

Early in May the GAO is to brief the Senate Armed Services Committee, according to agency sources. Meanwhile, executive branch agencies are being given the information.

"We still have a long dialogue going on," a Defense official said yesterday, "and the GAO is still out beating on the subject."

A GAO official said the study had "caused quite a bit of excitement." He hoped the Pentagon would soon come up with promised changes that could be made on the Mark 12A warheads that now are in production.