Foreign Minister Seiji Maehara summoned Russian ambassador Mikhail Bely and told him that the visit cast doubt on Moscow’s declared intention to improve relations with Tokyo.
Bely said that he called on Japan to “deal with it cool-headedly and in a balanced manner".
Russian Foreign Minister Sergei Lavrov responded by calling Japan's reaction "unacceptable" and saying Russia would summon Japan's ambassador to Moscow.
"As Japan has kept its position that the four northern islands belong to Japanese territory, the president's visit there is very regrettable," Prime Minister Naoto Kan told parliament.
The islands, which are north of Japan’s Hokkaido island, were seized by the Soviet Union at the end of World War II and have been controlled by Moscow ever since.
Japan claims the southernmost four as its territory.
The new row comes as Kan’s government is in trouble over its handling of a diplomatic row with China caused by a collision between a Chinese trawler and a Japanese coastguard vessel off disputed islets in the East China Sea.
Prosecutors freed the Chinese captain without charge but 30 MPs Monday claimed that a video shows the trawler deliberately ramming Japanese vessels.
Voter support for Kan’s government dropped 31 points in October, according to a poll by business daily Nikkei.
Sixty-five-year dispute over Kuril archipelago
The Soviet Union seized the Kuril Islands on 8 August 1945 just after Japan had surrendered to the US at the end of the Pacific War. Moscow had only declared war on Japan six days before the end of the conflict and after the atomic bomb was dropped on Hiroshima.
Japan had controlled all the1,300-kilometre-long volcanic archipelago since 1855 and refers to it as its Northern Territories.
The two countries have never signed a peace treaty to formally end World War II hostilities, largely due to the disputed islands.
The climate is harsh and the population is about 19,000 but the islands have mineral deposits, including gold and silver, and rich fishing grounds. They were home to Soviet air and sea bases during the Cold War.
The Soviet Union moved the 17,000-strong Japanese population to Kazakhstan and Uzbekistan.
In 1956 Moscow offered to give back the two smallest islands but Japan rejected the idea.
After the collapse of the Soviet Union talks on improving ties have resumed but no progress has been made, mainly because of the Kurils dispute.
The European Parliament backed Japan in 2005, calling on Moscow to hand back the islands.