According to Japanese Kyodo news outlet, the incident occurred at 2:00 a.m. local time (17:00 GMT), about 7 miles from Japan's easternmost city of Inubosaki.
As a result of the collision, one of the ships sunk. At the time of the incident, there were five crew members on the ship that sunk, four of which have gone missing.
Last year, the Japanese fishing boat carrying eight crew members on board collided with the South Korean trawler in the Sea of Japan, some 206 miles to the northeast of Dokdo (Takeshima) islands, contested both by Seoul and Tokyo.
Following the incident, the South Korean vessel started sinking, however, the 13-member crew was reportedly rescued.