The collision took place at around 9 a.m. in waters some 350 kilometers northwest of the Noto Peninsula in Ishikawa Prefecture, NHK and Kyodo News reported.
As the fishing boat began to sink, the North Korean crew jumped into the water before Japanese patrol and maritime safety authorities arrived alongside the vessel, the reports said.
The rescued crew members were then handed over to a number of North Korean ships that were nearby, while the damaged boat disappeared under the water some 20 minutes after the mishap.
The collision took place in Daehwatoe, one of the most important fishing grounds in the East Sea, about halfway between North Korea's east coast and Japan's lower west coast. North Korean fishing boats have often operated in the area, most of which is under the joint control of South Korea and Japan.
The Japanese Fisheries Agency was later reported to claim that the North Korean squid fishing boat was operating illegally inside Japan's exclusive economic zone.
Tokyo said the collision took place as its maritime regulators were chasing the boat away.
The EEZ is a sea zone over which a country has special rights regarding the exploration and use of marine resources. It stretches out to 200 nautical miles from the coastline.
But the North has disputed Japan's exclusive rights over the area, having dispatched an armed ship to the area in August to dispel Japanese patrol vessels away from what it claims to be its own EEZ. (Yonhap)