Japan on Thursday moved closer to charging a US military base employee with the rape and murder of a local woman on the southern island of Okinawa.

Kenneth Franklin Shinzato, 32, a former US Marine employed at the US Air Force's sprawling Kadena Air Base, was first arrested last month for allegedly disposing of the body of the victim, identified by local media as Rina Shimabukuro.

On Thursday, as is common practice in Japanese law, he was again arrested, this time for the separate crime of the alleged rape and murder of the 20-year-old woman, said an Okinawa police spokesman.