The Soviet Union could complicate a U.S. missile defense with so many thousands of decoy warheads that Strategic Defense Initiative officials are now seeking a new type of exotic and expensive technology to distinguish decoys from actual warheads, the chief of the Pentagon's "Star Wars" program said yesterday.

Lt. Gen. James A. Abrahamson, the SDI chief, told a congressional subcommittee yesterday that "we have now come to the conclusion" that traditional surveillance satellites will not be able to detect the warheads as they travel through space amid decoys, balloons, chaff and other matter -- "a threat cloud," Abrahamson said, "of frightening proportions."

As a result, he said, the SDI may have to deploy space-based neutral particle beams that could "irradiate" the threat cloud and ground-based lasers that could nudge and jostle the decoys, so other weapons could distinguish and destroy the real warheads.

Abrahamson appeared before a House Armed Services subcommittee to defend President Reagan's $5.4 billion fiscal 1987 budget request for SDI. Last year, Congress gave the Defense and Energy departments $3 billion for the program.

Abrahamson disputed assertions that the budget requests are "unprecedented and cannot be spent prudently." In fact, he said, the SDI office committed 94 percent of last year's budget, more than the military services.

Despite the new evaluation of possible Soviet countermeasures to the program, Abrahamson was generally upbeat about its prospects. He said the SDI is ready to move from "technology development to major experiments" and he expressed impatience with those who continue to question its feasibility.

"I have to say, I'm frankly a little bored with some of the superficial criticism that still is going on," he said, citing specifically those who say that fast-burning Soviet rockets could escape detection or destruction by leaving the atmosphere quickly. "We have left all of that so far behind," he said, without explanation.

The "major experiments" include testing ground-based missiles that could knock out Soviet warheads leaking through space defenses; simulation of computer programs, which have been called a potential SDI Achilles' heel, in a major facility called a "national test bed"; improved technology, and eventually a "prototype satellite," to detect Soviet missiles on launch; and a prototype free electron laser, a weapon that eventually would be beamed from the ground via "relay mirrors" and "fighting mirrors" in space to burn through Soviet missiles.

Only such components of air-launched weapons as guidance systems will be fired, which Abrahamson said will keep the experiments within bounds of the U.S.-Soviet Antiballistic Missile Treaty.

"The integrated experiments are the logical next step," he said. "They were never portrayed as being inexpensive, but without them the probability of determining if the SDI is feasible is very low."

Abrahamson also acknowledged that success "in nearly every element of the program" depends upon inventing better means of "space transportation and logistics." The newsletter Defense Week reported last month that, depending only on the space shuttle and other available rockets, 58 years and at least $87 billion would be needed to lift into space all of the weaponry currently part of Star Wars designs.

The general said that contractors are developing a missile that could be fired from the ground and destroy Soviet warheads as they reenter the atmosphere above the United States. He said such "exo-atmospheric" missiles could protect all of North America except Mexico from one site in North Dakota.

But current SDI designs also envision missiles that would destroy remaining warheads inside the atmosphere, closer to their targets. Those "endo-atmospheric" missiles would have to be deployed at "tens of thousands of sites" nationwide, a congressional aide said after Abrahamson testified.

Abrahamson said the SDI's implications for arms control and other strategic issues are more complex than the technical issues.