Medvedev arrived in Kunashir, one of the four islands just 10 kilometers off northern Japan, on his way back from his visit to Vietnam after attending an ASEAN summit held in Hanoi.
Japan, which also claims the Russian-held islands, has warned his visit would seriously hurt the two countries’ relations.
Medvedev is the first Russian leader, including those of the Soviet Union, to visit the islands, which Japan refers to the Northern Territories.
The Russian president had planned to visit the islands in September, but bad weather prevented him from doing so.
The islands were occupied by Soviet forces during the closing days of World War II. The two countries have not signed a peace treaty because of the row over the islands.