Russian Defense Minister Anatoly Serdyukov arrived in the southern Kuril islands to inspect a machine gun and artillery division and check on troops' combat readiness and living conditions, Russia's ITAR-Tass news agency said.
"We are planning to upgrade its weapons," Serdyukov said, according to state television.
Japan's Foreign Ministry said it confirmed that Serdyukov had arrived on the islands and lodged a protest with Moscow's ambassador in Tokyo that called the trip "extremely regrettable."
The group of four islands are called the Northern Territories by Japan, and the dispute over their ownership has prevented Tokyo and Moscow from signing a peace treaty formally ending their hostilities from World War II.
Although economic ties between Japan and Russia have grown, little progress has been made in resolving the island dispute, which remains a source of deep political tension and distrust between the two countries.
Russia has recently taken a more assertive approach to its claim.
Three months ago, Medvedev landed on the island closest to Japan, the first time a Russian leader has done so. Tokyo immediately protested, temporarily recalled its ambassador and warned against future visits.
Medvedev said afterward that he reserved to the right to visit the islands whenever he chose.
Serdyukov's trip comes a week before Japan's foreign minister is to visit Moscow, where the dispute is expected to be the focus of talks.
The islands are surrounded by rich fishing grounds and are believed to have offshore oil and natural gas reserves, plus gold and silver deposits.
They have been under Russian control since the waning days of World War II. They lie as close as six miles (10 kilometers) to Japan's Hokkaido island and are also near undisputed Russian territory.
Associated Press writer Vladimir Isachenkov contributed to this report from Moscow.