(AFP) A US Marine in Okinawa has been charged with non-consensual sexual intercourse resulting in injury, Japanese authorities said Friday, stoking discontent among residents over American military bases in the region.

The case came to light just days after it emerged that a US airman in Okinawa had been charged in March with raping a minor three months earlier.

Top government spokesman Yoshimasa Hayashi said local prosecutors had brought the new charge over another rape that allegedly took place in May.

In the latest case, the 21-year-old US Marine Corps member is accused of "assaulting the victim for the purpose of sexual intercourse and injuring her", an Okinawa police spokesman told AFP.

"The fact that he used violence for that purpose and wounded her constitutes non-consensual sex resulting in injury," the police spokesman said.

The woman had been "bitten in the mouth" and had taken two weeks to fully recover, he said. Media reports said she had also been choked.

The two cases have sparked outrage and echo Japan's fraught history with US troops, including the 1995 gang rape of a 12-year-old girl by three US servicemen.

Hayashi said on Friday the government has protested to US Ambassador Rahm Emanuel, calling for stricter oversight and steps to prevent a recurrence.

Details emerged this week of the alleged December incident in which a US airman was accused of raping a teenage Japanese girl.

In that case, the 25-year-old has been charged with assault as well as kidnapping for indecent purposes, said a spokesman at a court in Naha, Okinawa's main city.

Initial reports in that case had described it as sexual assault, although authorities confirmed it was being treated as rape.

Despite making up just 0.6 percent of Japan's landmass, Okinawa accommodates about 70 percent of all the US military bases and facilities in Japan.

"We take it very seriously that a sexual crime allegedly committed by an American soldier happened again after the December incident by the US airman," Hayashi said.

"It is our understanding that the United States also appreciates the extreme gravity of what happened," he said.

A litany of base-related woes has long grieved Okinawans, from pollution to noise and helicopter crashes, leading to complaints that they bear the brunt of hosting US troops.

"It's heart-rending to imagine how terrified and in despair the victim must have felt," Keiko Itokazu, head of an anti-base civic group, told reporters this week.

"Central governments in Japan and the US, as well as the American military, are pledging to reduce base-related burdens, but in reality turning a blind eye to the fact that our lives and safety are being threatened by these grave, malicious crimes," she said.