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.
A litany of base-related woes has long grieved Okinawans, from pollution and noise to helicopter crashes and COVID-19 outbreaks, leading to complaints that they bear the brunt of hosting troops.
The 1995 gang rape of a 12-year-old girl by three U.S. soldiers in Okinawa prompted widespread calls for a rethink of a 1960 pact that outlined the legal status of Japan-based U.S. military personnel.