"You are going to pay for this and you're going to pay for your crimes in Iraq, too," Fischer said in a comment directed at Japan's Prime Minister Junichiro Koizumi and U.S. President George Bush, the Mainichi Daily News reported Thursday.
Fischer made the threat during an interview from his detention center on Oct. 2 to a Philippine radio station and posted on the Internet Thursday.
Fischer is being held at an immigration detention center, while he fights a deportation order issued Aug. 24. A Tokyo court last month granted an injunction against the execution of the order.
Fischer, who defeated Boris Spassky to win the World Chess Championship in 1972, was arrested July 13 at Narita Airport for traveling on a revoked U.S. passport.
Fischer is wanted in the United States since a 1992 grand jury indicted him for playing chess in Yugoslavia in alleged violation of sanctions placed on the country at the time.