The Japan Coast Guard had rescued about 60 crew members from a North Korean fishing vessel which collided with a Japanese Fisheries Agency patrol ship.
The two ships collided in the Sea of Japan at around 9 a.m., about 350 kilometres off the Noto peninsula in Ishikawa Prefecture.
Japan’s fisheries agency said it was calling on the North Korean boat to leave Japan’s exclusive economic zone, but the boat drew too close and made contact despite being warned away.
Local media said no crew members on the Japanese patrol vessel were injured.
The fisheries agency has been stepping up its efforts in recent years to crack down on illegal squid fishing in the area.
In late May and June, Japan’s coast guard drove more than 300 North Korean boats from the same waters.
On Russia’s side of the Sea of Japan, the authorities say they seized more than 40 North Korean boats in September alone, and detained over 700 people on suspicion of poaching.