The Japanese patrol vessel and the North Korean fishing boat collided in Yamatotai, one of the best fishing grounds in the Sea of Japan.
Yamatotai is about 300 kilometers from the Noto Peninsula in Ishikawa Prefecture, and is within Japan's exclusive economic zone.
In recent years, North Korean squid fishing boats have been illegally operating in the area from early summer to winter.
Japan's Coast Guard and Fisheries Agency have sent patrol ships to the waters to deter illegal fishing.
In August, a speed boat displaying what appeared to be a North Korean navy flag approached a Japanese coast guard patrol vessel. The speed boat was about 30 meters from the Japanese ship at one point.
The Coast Guard said a man on board the speed boat pointed a gun at the patrol ship during the encounter.