The US Navy waited until Monday to make the arrest in the Japanese capital Tokyo public, two days after it actually took place on Saturday.
"We are cooperating with Japanese authorities," read a statement by Naval Forces Japan spokeswoman Cmdr. Reann Mommsen. "Due to the ongoing investigation and privacy concerns, it would be inappropriate for us to comment on any additional details."
An unnamed US Navy official told Stars and Stripes that the victim was not Japanese. Tokyo police did not comment on the case’s details.
The news of the sexual assault case came shortly after Capt. Michael Donnelly, USS Ronald Reagan’s commander, lifted a short-term alcohol ban on the ship’s sailors. The ban was introduced on Sunday morning after an uptick in incident involving drunk American sailors.
Neither the arrest nor the drink ban among US troops in Japan were unprecedented and the public have on many occasions staged rallies urging the government to force out American troops from the country.
Anti-American sentiments have been specially high on Okinawa Prefecture, where thousands of US troops are stationed.
Japanese locals complain about allegations of sexual abuse by the American soldiers, and are involved in a row with the Japanese government over the planned relocation of the US camp on the island.
A US base employee was recently arrested following the rape and murder of a local woman. News of the arrest prompted a wave of anti-US protests.
Police found DNA matching the dead woman's in a car belonging to Kenneth Franklin Shinzato, a former US Marine who worked at the US Air Force's Kadena Air Base in Okinawa. The man is suspected of having murdered the victim and disposed of her body.
In early June, a US sailor was arrested for drunk-driving the wrong way down a street in the region injuring two people.
In 2013, two American sailors admitted to raping a woman in Okinawa a year earlier in a case that sparked huge anti-US sentiments in Japan.
The gang rape of a 12-year-old Okinawan girl by three US servicemen in 1995 also sparked mass protests.
Japan has also warned the US to review the safety of its military equipment in the country following a number of high-profile aircraft crashes.