Iwao Yorimoto, an official of the Komagome police station in Tokyo, said the Defense Agency identified the two doctors as 1st Lt. Akinobu Ueta, 27, and 1st Lt. Koichi Oshima, 26, of Japan's Ground Self-Defense Force.
Yorimoto declined to identify the American because police were still investigating the case against him. Yorimoto said only that he is unemployed and formerly worked at a securities company.
The American had invited Ueta, Oshima and the woman to a party at his residence in downtown Tokyo on July 7, together with more than 10 other people, Yorimoto said.
The rape is alleged to have occurred early in the morning of July 8, but it is not clear when the suspects were taken into custody.
The three have denied raping the woman, who is in her 30s, Yorimoto said.
It is the second time this month that an American has been accused of rape in Japan.
U.S. airman Timothy Woodland, 24, stationed on the island of Okinawa, was arrested earlier this month on accusations that he raped a Japanese woman. He denies the charge.
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