Four fishing vessels were taken to a Russian port on the Kamchatka Peninsula's northeast coast after being stopped in the Russian zone of the Bering Sea November 3 with a suspected undeclared catch.
One of the ships, the 5 Dairin Maru, was released the next day because its violations of catch limits were minor.
Criminal proceedings have been opened against Takagawa Masuo, the captain of the 53 Tomi Maru, which reportedly illegally caught over 25 metric tons of pollock, skate, sea bass, and salmon.
Russia estimates damages to be at least 8.5 million rubles ($318,000), and the captain is facing up to five years in prison under Russian legislation.
Russia has also opened proceedings against the ship's owner, Kanai Gyogyo, based in Japan's Hokkaido. The trial could lead to the seizure of the trawler and the catch.
The Gyokuryu Maru and the 5 Yokei Maru are still being inspected. Russian authorities said preliminary checks have revealed 47 metric tons of illegal sea-catch on the former, and 7.9 metric tons onboard the latter trawler.
The trawlers are being unloaded, but the effort has been suspended over an approaching cyclone.
The crews will stay aboard their vessels until the checks are completed. A Japanese consulate official is monitoring developments.
Confrontations over poaching between Russian authorities and Japanese fishing vessels are frequent in Russia's Pacific waters.
An incident near the Kuril Islands, some of which are in territory claimed by both Russia and Japan, in mid-August led to the death of one Japanese fisherman, who was inadvertently killed when Russian border guards fired warning shots when the ship refused to stop.
