The Russian Justice Ministry announced on Tuesday that it designated as an "undesirable organization" a Japanese group seeking the return of four Russian-controlled islands to Japan.
Japan claims the four islands it calls the Northern Territories. The Japanese government maintains the islands are an inherent part of Japan's territory. It says the islands were illegally occupied after World War Two.
Russia made the move on Monday, possibly targeting a Japanese group called Hoppo Domei.
According to Russian media, any group designated as such is effectively banned from activity inside Russia.
Last April, Russian authorities labeled another Japanese group, the League of Residents of Chishima and Habomai Islands, which includes former islanders, an "undesirable organization."
Russia unilaterally announced it was suspending peace treaty negotiations with Japan, including talks over the islands. This was in response to sanctions imposed by the Japanese government over Russia's invasion of Ukraine.
Exchange programs for former residents of the islands also remain halted.
It has also been suggested that Russian President Vladimir Putin will someday make his first visit to the islands.
Japan's Chief Cabinet Secretary Hayashi Yoshimasa revealed the Japanese government lodged a protest on Wednesday through diplomatic channels and demanded that Russia retract its decision, calling it unilateral and unacceptable.
Hayashi added that the government will respond appropriately to ensure there is no negative impact on the activities of people campaigning for the islands' return.