About 20 members of the North Korean fishing boat fell into the sea after the collision that occurred at 9:10 a.m. on October 7.
The incident occurred about 350km northwest of Noto Peninsula, Ishikawa Prefecture, Kyodo News reported, citing information from the Japanese coast guard.
The South Korean ship involved in the collision was a semi-underground ship. No one on the Japanese ship was injured, according to a Japanese official and Coast Guard.
The patrol boat is trying to rescue the crew members on the fishing boat.
The Japanese Fisheries Agency said its patrol vessel had warned North Korean fishing vessels to leave the area before the collision.
The incident occurred near the Yamatotai area - a fishing area with rich seafood reserves in the Japanese Sea. The Japanese Coast Guard has also deployed more patrol vessels and a plane to the scene.
The Japanese government has set up a communications unit at the Prime Minister's crisis management center to handle the incident, according to Kyodo News.
