Russia said the Kurils dispute can be solved by "strengthening trust and mutual understanding." It also called on Japan not encourage the growth of confrontational attitudes among the younger generation.
The Japanese government announced earlier this week that new teaching guidelines for schools would state that the islands are illegally occupied.
Japan's actions, Moscow said, "contribute neither to the development of positive cooperation between the two countries, nor to the settlement of the dispute."
Before the recent G8 summit, held in Japan on July 7-9, Russia reaffirmed its sovereignty over the Southern Kurils, but said it was ready for talks with Japan on territorial issues.
The lower part of the chain of islands in question, stretching from the Kamchatka Peninsula on the Russian mainland to the north-east coast of Japan's Hokkaido Island, was annexed by the Soviet Union after World War II. The dispute has prevented the two countries from signing a formal peace agreement.