Three of the crew have already been rescued and returned to North Korea in line with their wishes, the coastguard said.
The troubled boat was spotted yesterday by a Japanese Self Defence Force jet patrolling the Sea of Japan (East Sea).
The coastguard launched a patrol boat and aircraft and found the fishing vessel at around 3:40 PM yesterday in waters 360 kilometres northwest of the Noto Peninsula in Ishikawa Prefecture.
The coastguard rescued three men clinging to the hull of the upturned boat.
A coastguard spokesman told AFP that five patrol vessels and one plane had been deployed to search for the missing fishermen.
"They have told investigators that they were on their way home after working," the spokesman said of the rescued men, without giving further details.
Japan and North Korea have tense relations, with Pyongyang routinely issuing verbal threats as well as firing missiles near or above Japan.
But the Japanese coastguard occasionally rescues North Korean fishermen in maritime accidents in regional waters.
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