Okinawa was the site of a brutal World War II battle between Japan and the United States but is now considered a strategic linchpin supporting the two countries' decades-long security alliance.
More than half of the 47,000 American military personnel in Japan are stationed there and rapes and other crimes by US service personnel have sparked local protests in the past.
The Naha district public prosecutors office on the island charged Justin Castellanos, 24, stationed at the US Marine Corps Camp Schwab base on the island, with the alleged crime, Jiji Press and other media reported.
A prosecution office spokesman declined to confirm the indictment by phone to AFP, while confirmation from the US Navy in Japan was not immediately available.
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A brutal 1995 abduction and rape of a 12-year-old girl on Okinawa by three US servicemen sparked massive protests, prompting Washington to pledge efforts to strengthen troop discipline to prevent such crimes and reduce its footprint on the island.
But continued crimes by US personnel remain an irritant in Japan-US relations and a rallying point for Okinawans and others in Japan opposed to the bases on the crowded island, where pacifist sentiment runs high.