Sunday morning, 39 Japanese boats entered Russian waters and remained there for an hour until a Russian patrol boat arrived. Russia protested to the Japanese authorities over the incident.
However, Mikhail Kamynin, the Foreign Ministry's official spokesman, said the boats had acted in accordance with a 1981 agreement between Japan and the USSR on the harvesting of seaweed.
The spokesman said: "We consider the issue closed, but the question of illegal fishing by Japanese boats remains. We continue to call on Tokyo to take all necessary measures to prevent illegal fishing by Japanese vessels in Russian waters in the future."
The latest incident came after Russian border guards shot dead a crewmember of a Japanese vessel near the Kuril Islands August 16. Russian officials said the vessel was suspected of illegally fishing for valuable crab in Russian territorial waters and that border guards had fired warning shots only after it had refused to stop.
Relations between Russia and Japan have long been strained over the Kurils. Japan maintains their seizure by the Soviet Union at the end of World War II was illegal, and the dispute has kept the two countries from signing a formal peace treaty.