Okinawa was the site of a brutal World War II battle but is now considered a strategic linchpin supporting the two countries' decades-long security alliance.
More than half of the 47,000 US military personnel in Japan are stationed there and rapes and other crimes by service personnel have sparked local protests in the past.
Foreign Minister Fumio Kishida yesterday summoned US ambassador Caroline Kennedy to the foreign ministry in Tokyo shortly after Okinawa police arrested a 32-year-old civilian US base worker in connection with the death of a missing 20-year-old Okinawa woman.
Kennedy replied that the US side would fully cooperate in the investigation, local media said.
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Police arrested Kenneth Franklin Shinzato, who lives in southern Okinawa and works at the US Air Force's Kadena Air Base, for allegedly disposing of the woman's body.
Local media said police also suspect the former US Marine murdered the victim, identified as Rina Shimabukuro, who had been missing since late April.
Her body was found in a weed-covered area in southern Okinawa after investigators conducted search based on his deposition, while police found DNA matching Shimabukuro's in the man's car, Kyodo news agency said.
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.
The arrest came ahead of Obama's trip to Japan next week to attend a Group of Seven summit and to make a landmark visit to Hiroshima.