The North Korean boat had made an unauthorized entry into the Japan's exclusive economic zone and the collision occurred just as the Japanese patrol boat was warning it to move out, Fisheries Agency official Satoshi Kuwahara told reporters. He said officials were investigating if the North Korean ship was actually carrying out illegal fishing, and how the two ships collided.
The Coast Guard office in Niigata said officials handed the fishermen to other North Korean boats in the area after notifying Pyongyang's rescue coordination center to arrange their way home. It said the North Korean crewmembers had no life-threatening conditions.
Fisheries Agency officials said the Japanese patrol ship had no major damage and was able to move on its own.
The collision site near Yamatotai is disputed between Japan and North Korea, which have no diplomatic ties.
The two countries also have disputes over Japan's 1910-1945 colonial rule of the Korean Peninsula, as well as North Korea's nuclear and missile development and the issue of the North's abduction of Japanese citizens in the 1970s and 1980s.
During Monday's parliamentary session, Prime Minister Shinzo Abe pledged to thoroughly investigate Monday's incident.
"We will resolutely respond to prevent poaching by foreign fishing boats in the Japanese exclusive economic zone," he said.
Japan has stepped up patrols in the area in recent years as North Korean squid poaching has surged. This year, ships from Japan's Fisheries Agency and coast guard have been patrolling in the area since May, Kuwahara said.
Japanese fisheries patrollers have issued nearly 500 expulsion orders to poachers between May and August this year, most of them from North Korea, according to the Fisheries Agency. It said Japan last year made 5,315 such orders to foreign fishing boats in the area, many of them North Korean.
Experts say the increase in North Korean squid poaching is due to the country's campaign to boost fish harvests. The poachers are believed to be related to an influx of ghost boats that have washed onto Japan's northern coast, fisheries officials have said.
In June, Japan's coast guard pushed more than 300 North Korean boats back from the same waters where Monday's incident occurred. Japan also said an armed North Korean fishing boat aimed a gun at and "threatened" a Japanese patrol ship in August.
- AP