The United States has around 54,000 military personnel stationed in Japan -- mostly on the subtropical southern island of Okinawa, to the east of Taiwan.

"A US marine in his 20s is suspected of raping a Japanese woman at an American military base in March, and is also suspected of injuring another woman," a local police official told AFP.

The second marine, also in his 20s, is suspected of raping a Japanese woman at a US base in January, the official said.

Police have referred the two cases to prosecutors.

Washington will cooperate "fully" with Japanese authorities in the investigations, said US ambassador George Glass.

"We deeply value the ties of trust and friendship we have built over many decades with our Japanese hosts, and I am committed to doing everything I can to prevent actions that may jeopardise these bonds," he said in a statement.

On Friday, US service members joined Japanese officials and residents in Okinawa for a one-off joint nighttime patrol along a downtown street dotted with bars.

The patrol -- the first such joint operation since 1973 -- followed other sexual assault cases in Okinawa involving American servicemen.

A 21-year-old marine was charged with rape in June last year, just months after prosecutors charged a 25-year-old US soldier for allegedly assaulting a girl under 16.

Okinawa governor Denny Tamaki called the latest cases "deplorable" and said authorities would urge the US military to prevent similar incidents, Japanese media reported.

Japan's top government spokesman Yoshimasa Hayashi declined to comment on the cases at a regular briefing Thursday, but said crimes by US troops were "unacceptable".

The alleged rape in March took place in a restroom, and the woman injured was trying to stop the assault on the other woman, Japanese media said, citing police sources.

Relations have long been fraught between Okinawans and the US bases.

Last year, a total of 80 people connected to the US military were charged in Okinawa for various crimes, police said.

The 1995 gang rape of a 12-year-old girl by three US soldiers in Okinawa prompted a major backlash -- with calls for a rethink of the 1960 pact allowing the United States to station troops in Japan.