Investigators found evidence of two possibly rocket-propelled bombs at the site in Yokosuka, police said, without elaborating.
Local news reports said police were investigating if the blasts were aimed at the U.S. base. A Yokosuka police spokesman confirmed this was the nature of the investigation.
The spokesman, who declined to be named citing department policy, could not verify media reports that the roof of a house in the neighborhood was damaged in one of the explosions.
Yokosuka Naval Base officials have not released a statement and were unavailable for comment Saturday.
Earlier Friday, the U.S. Navy announced that the USS George Washington, a nuclear-powered aircraft carrier, was scheduled to arrive Sept. 25 in Yoyosuka, its new home port, about 30 miles south of Tokyo.
The planned arrival of the carrier has drawn criticism from Japanese living near the base who are opposed to the U.S. military presence in Yokosuka and the increased number of American sailors the ship would bring to the area. There are also concerns about a possible accident or leakage from the aircraft carrier's nuclear reactor.
The U.S. Navy disclosed in August that the USS Houston, a submarine, had leaked water containing radiation during several calls to Sasebo and Okinawa in southern Japan and Yokosuka between July 2006 and April 2008. But a Navy investigation concluded the leakage posed no danger to Japan.