The Maritime Self-Defense Force vessel, Ukushima, with about 40 crew members, first reported the blaze at 9:50 a.m. Sunday, about 2.5 kilometers from Oshima Island in Fukuoka Prefecture.
The missing sailor, identified as Petty Officer 3rd Class Tatsunori Koga, 33, was assigned to the engine room.
The fire was initially contained by another MSDF vessel, Toyoshima, at 2 p.m. but later rekindled and caused it to capsize shortly after midnight.
One crew member was hospitalized with non-life-threatening injuries, while about 40 others were safely evacuated to the Toyoshima.
The Ukushima was conducting routine drills en route to Kagoshima Prefecture from its base in Shimonoseki, MSDF officials said.
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