Action against Mr. Fischer appeared a virtual certainty after his brooding and bitter news conference in September in Sveti Stevan, Yugoslavia, 70 miles from the killing in Bosnia and Herzegovina, a former Yugoslav Republic. He produced a Treasury Department letter ordering him not to play and warning of possible prosecution, held it up and spit at it.

The indictment came as Mr. Fischer appeared ready to resume a more active playing schedule. When he captured the championship 20 years ago, his strategic brilliance and relentless accuracy earned him the reputation as one of the greatest chess players ever. His most recent performance reflected an inconsistent, though promising foray back into the game. Trial or Exile

Prosecutors said that since he had also violated a United Nations economic sanctions measure they would try to have him extradited if he traveled outside of the former Yugoslav federation, although experts in international law said that would be very difficult.

"Mr. Fischer faces the choice of returning to this country or being checkmated to Yugoslavia," said Jay B. Stephens, the United States Attorney in Washington, who said that the Government could also try to seize his winnings of $3.35 million and 10 percent of the match's royalties.

International law scholars expressed surprise that, of all the possible violations of the economic embargo by arms salesmen and other commercial ventures, the Administration had chosen to go after a former chess champion.