The archipelago, known in Russian as the Kuril Islands and in Japanese as the Northern Territories, lies off the northeast coast of Japan.
The four islands were captured by the Soviet military during the final months of the war, and have been held by Moscow since, in what Tokyo describes as an "illegal occupation".
The Russian prosecutor general's office said Monday it had declared the Tokyo-based Northern Territories Issue Association "undesirable", accusing the group of "wanting to rewrite history and encroach on Russia's sovereignty".
The association, established in 2003, is Japan's main advocacy group for the return of the islands and provides teaching material to children about the dispute using a puffin mascot named "Erika-chan".
Being declared "undesirable" makes anyone who works for or collaborates with the organisation in Russia liable to prosecution.
Russia had already banned another group, the League of Residents of Chishima and Habomai Islands, which organised annual trips to the archipelago by former residents.
The dispute has prevented Russia, the formal successor to the Soviet Union, from signing a World War II peace treaty with Japan, a major sticking point in their relations.
Since launching its offensive in Ukraine in 2022, Moscow has waged an unprecedented crackdown on dissent that rights groups have likened to Soviet-era mass repression.
Among other organisations labelled as "undesirable" in Russia are the World Wildlife Fund, Greenpeace, Transparency International and Radio Free Europe/Radio Liberty.
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