Coastguard boats continued battling the blaze on the Sunflower Daisetsu after a distress call was made yesterday evening as it was sailing about 55 kilometres off the coast of Hokkaido, Japan's northernmost island.
"The fire has yet to be brought under control but the vessel remains stable while its location is unchanged offshore," a coastguard spokesman said.
A total of 94 people were aboard - 71 passengers and 23 crew members - when the fire broke out on the 11,401-tonne ferry, said an official of MOL Ferry, which owns the vessel.
The missing crew member was identified as Kunihiko Orita, a 44-year-old second officer, the MOL Ferry official said.
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The coastguard spokesman said: "We sent six members of the special search and rescue unit to the ferry today morning and they started searching for the officer on board."
The Japanese coastguard has said flames were spotted coming from a truck aboard the ferry and that it was working to put out the blaze.
It was not immediately clear how the fire broke out.
The ferry, which was carrying more than 100 transport truck trailers, cars and motorcycles, had left from a port northeast of Tokyo earlier Friday bound for the city of Tomakomai, a trip of several hundred kilometres.