Prosecutors in the southern island region charged the US soldier in March, top government spokesman Yoshimasa Hayashi told reporters on Tuesday.

Local media said the 25-year-old man had been accused of assault, adding that he knew the girl was under 16, the age of consent in Japan.

The government expressed "regret" to US Ambassador Rahm Emanuel over the incident and called for stronger oversight of behaviour by military personnel, Hayashi said.

Okinawa accounts for just 0.6 percent of Japan's land mass but hosts about 70 percent of all the US military bases and facilities in the country.

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 troops.

The 1995 gang rape of a 12-year-old girl by three US soldiers in Okinawa prompted widespread calls for a rethink of a 1960 pact that outlined the legal status of Japan-based US military personnel.

Okinawa governor Denny Tamaki voiced his "strong indignation" at the latest case.

"That something like this was done to a minor not only causes great fear to local residents living side-by-side with US bases but tramples on the dignity of women", he told reporters.

"The excessive burden of hosting military bases is an everyday matter for us, and is intolerable."

Anti-base sentiment in Okinawa has been displayed in particular over a plan to relocate the US Marine Corps Air Station Futenma.

While the central government wants to move the base to a less populated part of Okinawa's main island, many locals would prefer it be transferred elsewhere in the country.

A nationwide poll by broadcaster NHK in 2022 found 80 percent of Japanese consider the current disproportionate distribution of United States forces "wrong" or "somewhat wrong".