Bobby Fischer, the mercurial chess master who returned to the game professionally in September after 20 years, was indicted today on charges that he had violated economic sanctions against Yugoslavia by playing a match there.

A Federal grand jury here handed up the single-count indictment that accused Mr. Fischer of violating an executive order issued by President Bush in June that restricted commercial relations with what remains of Yugoslavia.

In the match, Mr. Fischer defeated the Russian-born grandmaster Boris Spassky in an exhibition rematch of their celebrated 1972 world championship.

Immediately after the indictment, Federal officials issued a warrant for his arrest.

Mr. Fischer, who was believed to be in the former Yugoslav federation, faces the choice of living in exile or returning to the United States for a trial that could result in up to 10 years in prison and a fine as high as $250,000. Prosecution No Surprise

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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.