Police district commissioner Olafur Helgi Kjartansson said Fischer's corpse was dug up from a cemetery near Selfoss in southern Iceland early yesterday in the presence of a doctor, a priest and other officials.
Kjartansson said Fischer was reburied after DNA samples were taken.
Fischer died in Iceland in January 2008 at age 64. He left no will, and legal wrangling continues over his estate.
Last month, Iceland's supreme court ruled Fischer should be exhumed so DNA testing could determine whether he was the father of Jinky Young, whose mother Marilyn says she had a relationship with Fischer. Jinky, who lives in the Philippines with her mother, flew to Iceland to provide her own blood sample in December.
Fischer became an American hero, but his later life was dominated by his eccentric behavior. He lost his world title in 1975 after refusing to defend it against Anatoly Karpov. He dropped out of competitive chess and largely out of view, spending time in Hungary and the Philippines, emerging occasionally to make outspoken comments, sometimes attacking the United States.
Fischer was arrested in Japan in 2004 and threatened with extradition to the United States to face charges of breaking international sanctions against the former Yugoslavia by playing a match there in 1992. He renounced his U.S. citizenship and spent nine months in custody before chess-loving Iceland granted him citizenship.
Fischer lived in Iceland from 2005 until his death and is buried about 30 miles east of the capital, Reykjavik.