US authorities have handed a sailor suspected of involvement in a local women's death to Japanese officials.
The USS Kitty Hawk is based in Yokosuka
William Reese, 21, was arrested by Japanese officials after being escorted to a police station in Yokosuka, south of the capital Tokyo.
The sailor, based on the USS Kitty Hawk aircraft carrier, has been under investigation following the death of Yoshie Sato.
The 56-year-old died on Tuesday after being found beaten and unconscious.
Mr Reese, who has been in Japan with the US Navy since May 2004, is expected to be questioned over several days.
The US Navy has pledged to continue to co-operate with Japanese authorities.
"The US Navy's responsibility to see this matter through to its rightful conclusion does not end here," Rear Admiral James Kelly said in a statement.
The case comes as the US is trying to win local support to station a new nuclear-powered aircraft carrier at Yokosuka.
Analysts say this recent incident could complicate sensitive negotiations between Washington and Tokyo over the redeployment of US forces.
About 50,000 US troops are stationed in Japan under a joint security pact, but Tokyo and Washington agreed late last year to remove 7,000 marines and shift other remaining troops within Japan.
Incidents involving US troops and local Japanese are particularly sensitive because of a 1995 case on the island of Okinawa when three US servicemen raped a schoolgirl.