"I decided to recall ambassador to Russia [Masaharu] Kono temporarily," Foreign Minister Seiji Maehara told reporters on Tuesday, adding he was waiting for more information from the ambassador.
Medvedev visited a disputed islet in the Kuril Islands Monday, a visit that was condemned by Tokyo as "very regrettable".
The Kuril Islands, north of Japan's Hokkaido island, have been controlled by Moscow since they were seized by Soviet troops at the end of World War II. Tokyo claims the four southern islands as Japanese territory.But Tokyo on Tuesday said Prime Minister Naoto Kan is still likely to meet Medvedev when he visits Japan for the Asia-Pacific Economic Cooperation (Apec) forum summit on 13-14 November.
Maehara says Tokyo would "seek to resolve the territorial issue".
The Japanese government is also involved in a diplomatic row with China over disputed islets in the East China Sea, which caused a 31-point drop in support for Prime Minister Naoto Kan’s government in October, according to an opinion poll by the business daily Nikkei.
On Tuesday Beijing rejected a US offer to mediate in that dispute, saying that China and Japan alone should resolve the disagreement.