Kenneth Franklin Shinzato, 32, a former US Marine employed at the US Air Force's sprawling Kadena Air Base, was first charged in early June for allegedly disposing of the body of the victim, identified by local media as Rina Shimabukuro.
As is common practice in Japanese law, he was again charged by Okinawa prosecutors, this time for the separate crime of the alleged rape and murder of the 20-year-old woman, Jiji Press and other news reports said.
The case has intensified longstanding local opposition to the American military presence on the strategic island, which reluctantly hosts nearly 75 per cent of land alloted for US bases in Japan even though it accounts for just a fraction of the country's total area.
Crimes by US personnel have long sparked protests on crowded Okinawa, and have been a frequent irritant in relations between close security allies Japan and the United States.
Shinzato's initial arrest in May sparked fresh anger among Okinawans as well as a harsh public rebuke by Japanese Prime Minister Shinzo Abe to US President Barack Obama when he visited Japan for a Group of Seven summit.
More than half the 47,000 American troops in Japan under a decades-long security alliance are stationed on Okinawa, the site of a major World War II battle that was followed by a 27-year US occupation of the island.
A series of crimes including rapes, assaults, hit-and-run and drink-driving accidents by military personnel, dependants and civilians, has long sparked protests.
In mid-June, tens of thousands rallied on the island to protest against the heavy US military presence and violent crimes by American personnel.
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