Japanese ambassador will be summoned to the Russian Foreign Ministry over Tokyo's reaction to Medvedev's visit to Kuril Islands, Foreign Minister Sergei Lavor was quoted by local media as saying on Monday.
The minister told a press conference that Japanese's reaction to Medvedev's visit was "unacceptable", adding that "this is our land and the Russian president visited Russian land."
Leonid Slutsky, first chairman of the State Duma committee on international affairs, also said Japanese authorities' reaction to Medvedev's visit was "inappropriate."
"The issue of a protest note to the Russian ambassador to Japan in connection with this situation cannot be regarded as anything but Japan's inappropriate reaction to the Russian president's visit to the Kuril Islands," Interfex news agency quoted Slutsky as saying.
Russian President Dmitry Medvedev on Monday morning visited Kunashiri Island, one of the Russian-held islands also claimed by Japan, Russia's local media said.
Medvedev is the first leader from Russia or the former Soviet Union to travel to any of the disputed islands, which are called the Northern Territories in Japan and the Southern Kurils in Russia.
Upon Medvedev's arrival on the islands, Japanese Foreign Minister Seiji Maehara summoned Russian ambassador to lodge a protest against the visit.
The Russian envoy, however, insisted that the president's visit is Russia's domestic issue, according to the report.
The four disputed Pacific islands were occupied by the Soviet troops in 1945 and are currently under Russian control.
Russia and Japan have long been at odds due to the territorial dispute over these islands, which has blocked a peace treaty between the two countries since the end of World War II.