"Naval Criminal Investigative Service () is investigating Yokosuka-based sailors for alleged drug use and distribution," the 7th Fleet said, referring to its home base southwest of Tokyo.
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"The Navy has zero tolerance for drug abuse and takes all allegations involving misconduct of our sailors, navy civilians and family members very seriously," it said in a comment emailed to AFP.
It added the allegations were still under investigation and would not comment further.
The response came after the Wall Street Journal reported that at least a dozen sailors were being investigated on suspicion of buying, selling and using LSD, ecstasy and other drugs.
Some of them were serving aboard the USS Ronald Reagan aircraft carrier whose home port is Yokosuka, the journal quoted navy officials as saying Friday.
The navy was also probing whether US sailors were using the internet to buy or sell drugs or were distributing them to local Japanese residents, it said.
The drug allegations come at a time when Japan is touting its security alliance with the United States to counter missile and nuclear threats from North Korea.
The 7th Fleet has also been hit by a string of accidents in the last year.
In August, the destroyer USS John S. McCain collided with a tanker off Singapore, killing 10 sailors and injuring five others.
Two months earlier in June, another destroyer, the USS Fitzgerald, and a cargo ship smashed into each other off Japan, leaving seven sailors dead.
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