Japan lodged a protest with the US embassy over the alleged rape of a Japanese woman by an American Marine at the Okinawa military base, the media reported on Monday.
"It was extremely regrettable that this case happened," said Yoshihide Suga, the government's top spokesman.
The government has asked the US to "tighten discipline and prevent a recurrence of such incidents", he added.
The rape allegation come amid a controversy surrounding the relocation of the US military base in Futenma to another complex in the northern part of the island, further away from urban centres, EFE news reported.
US authorities have promised to take up the case seriously, the official said, adding it would be "regrettable" if a US official was found guilty of rape.
The 24-year-old US sailor allegedly raped a 40-year-old Japanese woman on Sunday in a hotel in Naha city. The Marine, arrested on Sunday evening, has denied the rape charges.