Japanese and US base firefighters held off battling the fire as the contents of the building were assessed, and the blaze died out on its own about six hours after it started shortly before 1:00 AM (2130 IST) with firefighters standing by to contain the blaze.
The explosion occurred at the US Army Sagami General Depot in the city of Sagamihara, 40 kilometres southwest of the Japanese capital, Japanese officials and the Pentagon confirmed.
Several hours later, a huge blaze broke out at a steel pipe plant near Tokyo's Haneda airport - in the same prefecture - but local police declined to speculate on whether there was any link between the two incidents.
"We do not know any details at this point," a police spokesman told AFP on the question of any connection.
Nearly 600 people work at the facility which stores supplies and acts as a repair centre for military vehicles.
Dramatic video footage showed large sparks - possibly metal canisters - shooting out like fireworks from a huge fire on the building's roof, lighting up the night sky.
A woman who saw the aftermath of the blast told public broadcaster NHK that she heard repeated thunderous explosions for 10 to 15 minutes.
"Orange sparks were rising quite high. I couldn't see smoke but smelled something like gunpowder," she told NHK.
"I thought the American military facility came under a terrorist attack," a local security guard told Jiji Press news agency.
The Pentagon said the cause of the explosion was not immediately known, but that the building did not store ammunition or "radiological materials". Nearby buildings were not damaged.
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