Local authorities said Kenneth Shinzato, a former Marine, now faces the murder and rape charges in addition to an earlier charge of abandoning the victim's body. The woman was found dead in a forest last month, three weeks after she had disappeared while taking a walk.
The case has sparked outrage on Okinawa, where residents have long complained about its heavy US military presence and crime linked to them. The subsequent arrest and indictment of a US sailor for alleged drunken driving has added to the anger.
Critics want the air station completely removed from the island.
Half of about 50,000 American troops stationed in Japan under a bilateral security agreement are based on the island.
The US military says the crime rate among its ranks in Japan is lower than among the general public.
Prime Minister Shinzo Abe's government, which wants Japan to play a bigger military role internationally, backs the Japan-US security alliance.