Fischer, who is wanted by US authorities for attending a 1992 chess match in Yugoslavia in violation of international sanctions, was stopped at Tokyos Narita International Airport on Tuesday, an airport spokesman said on condition of anonymity.
Fischer, 61, was attempting to leave Japan for the Philippines, the spokesman said.
Filipino Grandmaster Eugene Torre, a long-time friend of the reclusive chess genius, said he was surprised to learn that Fischer has been held and that he was heading to Manila.
"Actually, we havent talked for around two years. Nagtatampo sa akin yan kasi akala niya close na kami ni Campo when I assumed the presidency of the NCFP (National Chess Federation of the Phils.)," said Torre, referring to former FIDE president Florencio Campomanes.
The Baguio-based Torre, who served as Fischers second when the latter briefly came out of reclusion in 1992 to play Boris Spassky whom he beat for the world title in 1975, has hosted Fischer in Baguio a number of times.
In fact, the two are linked not only by the sport but also with promoting a variation of the ancient game they called random chess.
Fischer was detained on suspicion of violating immigration laws, and officials were preparing to deport him to the United States, said the Asahi Shimbun Friday, a major daily, citing unnamed sources.
However, in Fischers website, it was reported that "he has been viciously attacked, brutalized, seriously injured and very nearly killed when he was illegally detained and arrested by the Japanese immigration authorities at Narita international airport in Tokyo Japan."
The website also said the former world champ was urgently requesting for immediate offer of "political asylum from a friendly third country."
The US Embassy in Tokyo said they were aware of Fischers case.
"We are aware that Bobby Fischer has been detained," an embassy official said on condition of anonymity, declining to give further details citing privacy concerns.
Fischer, a chess prodigy, became grandmaster at age 15. He was world chess champion from 1972 until 1975, when he forfeited the title and withdrew because conditions he demanded proved unacceptable to the International Chess Federation.
After that he virtually disappeared, living in secret outside the United States.
He emerged in 1992 to play another former world champion, Boris Spassky, in a highly publicized match in Yugoslavia. Fischer beat Spassky, 10-5, to win $3.35 million.
The US government accused Fischer of violating UN sanctions against Yugoslavia by playing the match. The sanctions were imposed on Yugoslavia for provoking warfare in neighboring Bosnia-Herzegovina. with reports from Dante Navarro