The United States ambassador to Japan vowed "complete and unequivocal cooperation" Wednesday over the alleged rape of a local woman by two servicemen on an island already fed up with the US military.

Ambassador John Roos moved swiftly to reassure people on the southern Japanese island of Okinawa that he shared their anger over an incident that has the potential to act as a lightning rod for growing anti-US feeling.

Roos said the US government and military would "provide full, complete and unequivocal cooperation to the Japanese authorities in their investigation".

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."

He said he wanted the Japanese people to know that he shared that anger.

"Not only me as a United States ambassador, but the entire United States government including our military will continue to work our hearts out to earn the trust of the Okinawan people and the people of Japan," he said.

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

Citing another case of sexual offence 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".

The arrest of the two men on Tuesday is a potential flashpoint in relations between the US military and their reluctant Okinawan hosts.

Previous criminal incidents have sparked angry, large-scale demonstrations, with participants demanding a cutting back of the US presence. 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 centre 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 and calling for mainland Japan to step up to the plate.

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.

Despite the groundswell of opinion, the strategic importance of the Okinawan archipelago, which is strung out from the Japanese mainland to Taiwan, makes it a vital bulwark against the rising might of China.

Neither Washington nor Tokyo, which depends on its ally for defence, is able to countenance a sizeable US drawdown from the area.

Okinawa police said they arrested Christopher Browning and Skyler Dozier Walker, both 23, on charges of raping and injuring the woman on Tuesday, hours before they had reportedly planned to leave the island.

The local woman, whose identity was not revealed, suffered injuries to the neck, police said.

The leading Mainichi Shimbun daily, citing police sources, said the two servicemen, who had flown to Okinawa on Sunday, had allegedly approached the woman on the street and sexually assaulted her.