Two US servicemen were arrested on Japan's southern island of Okinawa on suspicion of raping a Japanese woman, police said on Wednesday, a case that could again strain Tokyo's ties with its closest ally, Washington.

The arrests come at a time when public opinion in Okinawa is at odds with Tokyo for allowing the US deployment of Osprey hybrid aircraft on the island despite lingering concerns about their safety.

Tuesday's arrests also coincide with a sharp deterioration in Japan's relations with China over the Diaoyu Islands dispute in the East China Sea.

Okinawa is major center for the US military based in Japan.

Friction over the US base on Okinawa intensified after the 1995 gang rape of a 12-year-old Japanese schoolgirl by three US servicemen. The case sparked widespread protests by Okinawans, who had long resented the US presence due to crime, noise and deadly accidents.

"I feel strong anger and indignation," Japanese Defense Minister Satoshi Morimoto told Okinawa Governor Hirokazu Nakaima, who described the incident as "madness".

"I will press the United States for measures to implement stricter discipline," Morimoto said.

US ambassador to Japan John Roos said in a statement that his government was extremely concerned by the incident and was committed to cooperating fully with the Japanese authorities in their investigation.

"I am also in close contact with the Commander, US Forces Japan. These allegations, given their seriousness, will continue to command my full personal attention," Roos said.

The two US servicemen are suspected of raping a woman early on Tuesday morning in central Okinawa, an Okinawa police spokesman said.

The case has been sent to Okinawa prosecutors, another police official said.

After a meeting with Vice-Foreign Minister Shuji Kira, who is standing in while Foreign Minister Koichiro Gemba is in Europe, Roos said: "I do understand the anger that many people feel with respect to this reported incident."

Nakaima, a vocal critic of the size of the vast US presence on the island, met Morimoto and expressed his fury, describing the alleged crime as "insane".

Citing another case of sexual offense allegedly by a US soldier in August, the governor told reporters: "This is nothing but abhorrent.

"We cannot accept this, no matter how much (the US military presence) is claimed to be necessary for national security," he said.

Prime Minister Yoshihiko Noda also chimed in, saying the alleged crime was "intolerable".

Previous criminal incidents have sparked angry, large-scale demonstrations, with participants demanding a trimming of the US footprint. Around half of the 47,000 military personnel Washington has in Japan are based in Okinawa.

Relations at the moment are especially prickly, with locals resentful of the deployment of 12 tilt-rotor Osprey aircraft.

Ostensibly, the objections center on the Osprey's perceived poor safety record, but commentators say it is a proxy issue for islanders fed up with what they see as an unequal burden.

In September tens of thousands of people rallied against deployment of the Osprey, which can take off and land like a helicopter, but flies like a plane.

Reuters-AFP