Fire took hold of the 497-tonne Cambodian-registered freighter, Taigan, which has been in the port of Wakkanai in northern Japan since Tuesday, said an official at the local coastguard office.
A total of 23 Russian and Ukrainian crew members were on the ship, which had transported crabs from a Sakhalin port. Six of them -- all Russian -- had been unaccounted for, the coastguard said.
"We have found six bodies in the ship and are now identifying them," the official said, adding that two other crew members were hospitalised for burns but neither was in a life-threatening condition.
The fire was put out by early afternoon today, the official added.