The protest over the disputed islands could set back Japanese Prime Minister Shinzo Abe's efforts to court resource-rich Russia and keep the door open to dialogue, despite the Ukraine crisis.
Tokyo and Moscow have been involved in a decades-old dispute over the islands north of Hokkaido, which are known in Russia as the Kuriles, and referred to as the Northern Territories in Japan.
Russia seized them in the waning days of World War Two and the dispute has kept the two countries from signing a formal peace treaty.
After Medvedev visited Iturup island on Saturday, senior Japanese Foreign Ministry Official Hajime Hayashi lodged the protest with the Russian ambassador to Japan, Evgeny Afanasiev, over the telephone, the Japanese ministry said.
Japanese Foreign Minister Fumio Kishida will delay a visit to Russia that had been arranged for the end of August, according to media reports.
Medvedev's visit is likely to have an adverse impact on Russia's relations with Japan, which had been looking to arrange a visit this year by Russian President Vladimir Putin for summit talks with Abe, as media reported.


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