The disagreement over the southern Kuril islands, known in Japan as the Northern Territories, has long been a sticking point between the two countries. It also has kept them from signing a formal peace treaty ending their World War II hostilities.
Medvedev told Cabinet ministers that Russia must strengthen its presence there and that the new weapons will protect the islands as an "inalienable part of Russia."
Several hours later, the state news agency ITAR-Tass cited a Defense Ministry source as saying that some of the four Mistral assault ships that Russia has contracted to buy from France would be deployed in the Pacific Fleet, in part to defend the southern Kurils.
The purchase of the Mistrals, which can carry up to 16 helicopters and dozens of armored vehicles each, was signed in January. The deal sparked concern in the United States, in the Black Sea nation of Georgia and in the former Soviet Baltic nations who are worried about Russia's sway over its neighbors.
Medvedev in November visited one of the Kuril islands, despite strong objections from Japan. It was the first trip there by any Russian or Soviet leader and underlined Russia's determination to hold onto the islands even as it tries to project a more cooperative image in foreign relations.
On Wednesday, he reaffirmed that determination, saying new weapons will be sent to "to guarantee the security of these islands, which are an integral part of the Russian Federation."
The four islands, seized by Soviet troops in 1945 in the last days of World War II, give Russia a military toehold just off the northeastern tip of Japan's northern Hokkaido Island.
The Russian president also said Wednesday the government may boost its funding of social and economic development of the sparsely populated islands, and suggested tourism possibilities could be developed.