The U.S. Navy 7th Fleet said the raised levels were detected on the aircraft carrier USS George Washington at Yokosuka Naval Base, the Stars and Stripes reported.
Elevated levels of radiation also were detected at the naval air facility at Atsugi, the report said.
The Navy said the elevated levels were associated with the disaster at the Fukushima Dai-Ichi nuclear power plant about 200 miles north of the bases. The plant has experienced a series of fires and explosions since a 9-magnitude earthquake struck Japan Friday.
In an announcement at the Atsugi facility, the base commander, Capt. Eric Gardner, said a third reactor at the Fukushima nuclear plant exploded and "[radiation] has been detected at extremely low levels at Yokosuka and Atsugi. Radiation is at the levels of a chest X-ray … ."
Residents initially were directed to remain indoors with the windows closed but later were told they could walk about the base, the Stars and Stripes said.
"We're not expecting this to last long," public affairs officer Tim McGough said. "Winds should be changing early this afternoon, we're told."
Officers with Camp Fuji, Camp Zama and Yokota Air Base, all near Tokyo, told the Stars and Stripes they had not detected elevated levels of radiation.