Omu Shyozo, the captain of the Gyokuryu Maru, was detained November 2 off Russia's Kamchatka Peninsula with illegal catch along with two other Japanese fishing vessels.
"The court has found the captain guilty of committing an administrative offense by illegally catching over 122 metric tons of pollack in Russia's exclusive economic zone," the local prosecutor's office said.
Prosecutors said criminal proceedings against Kanai Gyogyo, the owner of the three vessels based in Japan's Hokkaido, were continuing despite the court decision on one of the captains.
Tagawa Masuo and Soejima Kenzi, the captains of the Tomi Maru 53 and the Yokei Maru 5 ships respectively, are still under investigation facing poaching charges. The trawlers with the crews on board are anchored in Russia's Avachi Bay.
Prosecutors said the crewmen were free to return home. "[They] are absolutely free and can go home whenever they like."
Confrontations over poaching between Russian authorities and Japanese fishing vessels are frequent in Russia's Pacific waters.
An incident near the Kuril Islands in August, some of which are claimed by both Russia and Japan, led to the death of a Japanese fisherman, who was killed when Russian border guards fired warning shots when the ship refused to stop.
