Authorities in Sakhalin in Russia's Far East say they will question the crew of the Russian vessel that collided with a Japanese fishing boat in the Sea of Okhotsk.
Three Japanese crew members died in the accident early on Wednesday off Japan's northernmost prefecture of Hokkaido.
The Russian Embassy in Tokyo posted a message on Facebook expressing heartfelt condolences to the families and relatives of the deceased.
It said Russian authorities are keeping close contact with the Japanese side to shed light on the circumstances of the accident.
Russia's state-run media say the Russian vessel, the Amur, was built in Japan in 1989, and is currently owned by the Amurskoye fishing company in Sakhalin. The ship is described as a medium-size trawler.
An official at Amurskoye told NHK the company is gathering information but has not been able to grasp the situation because the vessel in still in Japan. The official said the Amur was on its normal sea route.