Three of the crew have been arrested on suspicion of theft after they reportedly admitted to "taking out" electronic products from a remote Japanese island where they landed briefly to take refuge.
They are suspected of stealing a variety of items -- including fridges, TV sets and even a door knob.
The ten men were first spotted by coastguard as their dilapidated boated drifted into waters off the island of Hokkaido.
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"The immigration office in Hokkaido has started deportation procedures" for the six crew members, immigration official Koichi Tanaka told AFP.
One of the men is still in hospital, reportedly suffering from a stomach illness, said Tanaka.
Dozens of North Korean fishing vessels wash up on Japan's coast every year, but last month Japanese coastguards registered 28 cases, the highest monthly number since records began in 2014.
Experts say some North Korean fishermen are travelling far out to sea in order to satisfy government mandates for bigger catches.
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But their old and poorly equipped vessels are prone to mechanical and other problems, including running out of fuel, and there are few ways for them to call for rescue.
Some experts have warned that once they are deported, they may be executed as the North Korean authorities fear they must have been turned into Japanese spies.
"We decline to comment if they wish to go home or not," Shin Harada, another immigration official, told AFP.
"I've never heard about executions," he said.
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