In the latest of a string of incidents involving US troops, the man is accused of raping a Filipino woman at a hotel.
The alleged rape happened before a 24-hour curfew was imposed on US troops, their families and civilians working for the military on Okinawa.
The focus on crime by military personnel in recent days is affecting relations between Japan and the US.
Another American serviceman is accused of rape on Okinawa, the second alleged incident in 10 days.
The first complaint was made by a 14-year-old schoolgirl, the second by a woman from the Philippines who says she was attacked in a hotel.
n the last few days another soldier was found drunk asleep on a sofa in a house he had broken into, while another was arrested for drink-driving.
What is happening here is that a high-profile incident, the alleged rape of the schoolgirl, has focused an unusual amount of attention on the behaviour of the tens of thousands of US troops stationed on Okinawa.
Crimes carried out by US personnel there have always angered local residents.
Usually offences like drink-driving would get reported only in the local paper, but right now they are being reported around the world.
The US authorities know this is a problem.
High-ranking White House officials visiting Tokyo find themselves having to reassure their Japanese counterparts they are doing all they can to reduce the amount of crime.
A 24-hour curfew has been imposed, not just on servicemen but on their families and civilian staff too.
It aims to prevent US personnel drinking in bars or clubs and getting into trouble.
The military will be hoping that in time Japan's national media will lose interest in the story.
There is no evidence that more crimes are being carried out than before.Last year just 46 US military personnel were arrested on Okinawa in connection with criminal cases, a tiny proportion of those stationed there, and that figure was less than half the number five years ago.