Few details have been released over the latest case, other than that it involves an alleged attack on a Filipino woman at an Okinawa hotel, officials said on Thursday.
Japan's Kyodo news agency said the alleged assault took place on Monday and US military authorities had taken the serviceman into custody.
The 21-year-old Filipino woman was treated in hospital for unspecified injuries, Reuters quoted a US military spokesman as saying in an e-mail.
"I appreciate what is being done, although I want to see more concrete moves to prevent this happening again"
Nobutaka Machimura, Japanese chief cabinet secretary
She had reportedly been staying with a US serviceman in a hotel in Okinawa city.
The case is likely to fuel growing anger on Okinawa over the conduct of US servicemen following last week's rape charge and the arrests of two marines over the weekend, one accused of trespassing and the other of drink driving.
Christopher Hill, the US assistant secretary of state, said he has already expressed his regret in talks with a senior Japanese foreign ministry official about the issue.
The meeting with Shinichi Nishimiya, director-general of the ministry's North American affairs bureau, comes ahead of a scheduled visit by Condoleezza Rice, the US secretary of state.
"I expressed my great regret of the situation that has developed in Okinawa, my great concern about the feelings of the people of Okinawa and the fact that this is a very difficult time," said Hill.
Rice, who is due to arrive in Tokyo next week, is expected to face complaints about US military discipline.
Earlier this week, Yasuo Fukuda, the Japanese prime minister, said he would raise the recent incidents in Okinawa during Rice's visit and discuss ways to prevent a recurrence.
Locals in Okinawa, which hosts the bulk of the 50,000 or so US troops stationed in Japan, often complain about the noise, crime and pollution associated with the US bases.
Curfew on troops
The US military on Wednesday imposed a 24-hour curfew banning troops on the Japanese island from leaving their homes or bases except to go to work, to school, to places of worship or visit a doctor.
"This period of reflection will allow commanders and all service members an opportunity to further review procedures and orders that govern the discipline and conduct of all US service members serving in Okinawa," said US military said in a statement.
The move was welcomed by Nobutaka Machimura, Japan's chief cabinet secretary, who said it was a "meaningful" first step.
"I appreciate what is being done, although I want to see more concrete moves to prevent this happening again."