The 15,733-ton Fairy Angel, with a crew of 21 Filipinos, was on its way from Vancouver, Canada, to Chiba in Tokyo Bay carrying construction materials and other kinds of cargo on board, the official said.
The fire started in the ships engine room shortly after midnight, some 67 kilometers off Cape Choshi, east of Tokyo.
A 21-year-old worker, Christopher Castillo, was found dead in the engine room and second-class engineer Pergentino Agbon, 52, was missing after falling overboard, the official added.
The fire was put out in nine hours and the ship, which was not in danger of sinking, was being towed to Chiba by a salvage ship.