Two US Navy sailors were arrested in Okinawa over the alleged rape of a woman, local police said on Wednesday, with the incident likely to further strain ties between Tokyo and Washington.

Following the arrests, Japan's Senior Vice Foreign Minister Shuji Kira summoned US Ambassador to Japan John Roos to the Foreign Ministry to lodge an official protest over the incident and told Roos the allegations are both extremely serious and hugely regrettable.

Kira, stepping in for Foreign Minister Koichiro Gemba who is in Paris, also said to Roos that the United States had to do more than just merely enforce stricter discipline over its personnel stationed in Japan's southernmost prefecture to ensure there are no recurrences of such incidents.

Roos told Kira the US side would fully cooperate with the Japanese authorities' investigation and work hard to earn the trust of the people of Okinawa.

"It is the full intent of the US government to provide full, complete and unequivocal cooperation with Japanese authorities in their investigation of this matter," he said.

"We, as we have always done in the past will work our hearts out to earn the trust of the Okinawan people and the people of Japan as a whole," Roos said, adding that he understood the anger that many people feel with respect to this reported incident.

According to local police and US officials, the two US servicemen were arrested and detained on suspicion of raping a 27- year-old local woman during the early hours of Tuesday as she walked home from work in Naha, Okinawa's capital city.

Police also said a third man was arrested and subsequently released, but the two detainees, visiting from Fort Worth Naval Air Base in Texas, have been sent to prosecutors in Naha.

Seaman Christopher Browning, 23, denied the allegations while Petty Officer 3rd Class Skyler Dozierwalker, 23, admitted to them, police statements said.

The victim said the alleged attack took place in a parking lot near her home and lasted for 45 minutes during which she sustained multiple injuries.

The incident comes at a time when ties between Tokyo and Washington have become increasingly strained due to local officials and citizens of Okinawa seeking to lessen or be completely absolved of its US base-hosting obligations.

Around 75 percent of land in Okinawa is occupied by the US military, although the tiny island accounts for only 0.6 percent of Japan's total land mass.

Authorities and citizens of Okinawa have consistently complained about the military presence there, citing increasing issues of pollution, noise, accidents and crime.

According to Japan's defense ministry, 50 percent of crimes and accidents that take place on the island are linked to the US military, including the globally-publicized rape of a 12-year old girl by three US servicemen in 1995.

The latest incident in Okinawa comes at an already tense time between Tokyo and Washington, following the controversial deployment on Okinawa of the US military's accident-prone Osprey V-22 aircraft.

The arrival and deployment of the plane sparked widespread protests on and around the island by officials and citizens concerned about the plane's less-than-stellar safety record.

The safety of the tilt-rotor aircraft, manufactured by Bell Boeing, has been brought into question following an MV-22 Osprey crashing in Morocco in April last year, killing two Marines and another crashing in Florida in June, injuring all five crew members.

Prior to this and during the Osprey's developmental phase, 30 Marines died in three crashes, including 19 in a single accident in Arizona, in 2000 and more recently in 2010 an Air Force CV-22 touched down short of its landing zone in Afghanistan, hit a ditch, and flipped over, killing four of its occupants, according to official US military aviation sources.

The arrival of the controversial plane is a stark reminder for the people of Okinawa of when in August 2004 a Marine CH-53D Sea Stallion heavy assault transport helicopter crashed into Okinawa International University in Ginowan.

Okinawa Govornor Hirokazu Nakaima, a staunch advocate for both US military equipment and personnel being stationed off the island due to accidents, incidents of crime and other burdens shouldered by locals, on Wednesday suggested that Japan may need to rethink its security arrangement with the United States.

"Although I have asked repeatedly for a reduction in crimes and accidents perpetrated by US military personnel, it has happened again," Nakaima told reporters.

"Problems will always arise as long as the US-Japan Status of Forces Agreement (SOFA) remains unchanged," he said.

Nakaima who himself also lodged a protest at the USEmbassy in Tokyo on Wednesday, urged Japan's Defense Minister Satoshi Morimoto to seek a stern response to the matter from the US government.

Describing the alleged assault as "insane and abhorrent," and citing a previous sexual assault in Okinawa by a US soldier in August, Nakaima said that Okinawa cannot continue to accept this.

"No matter how much the US military presence is claimed to be necessary for national security, we simply can't go on accepting this," he said.

Morimoto for his part, while vilifying the rape suspects, suggested the US military is not training its service people correctly, if such crimes are continuing to occur at the frequency they do.

"This is an extremely egregious and vile incident. It goes way beyond the limits of what is tolerable. I feel that there must have been a failure in how the US military trained its personnel, " the defense minister said.

Similarly, Prime Minister Yoshihiko Noda called the incident " intolerable," while Chief Cabinet Secretary Osamu Fujimura described the case as being "extremely regrettable."

Recent media reports citing local sources state that there have been 127 cases of the rape of local women by members of the US military since 1972, with nine cases occurring in the past 10 years.