Medvedev visited Iturup (called Etorofu by the Japanese) island, the largest in the archipelago, marking his first trip to the disputed region since 2015 and his fourth overall, reports Efe news.
Japanese Foreign Minister Taro Kano said in a statement that Medvedev's visit was incompatible with Tokyo's position regarding the Northern Territories.
Northern Territories is the Japanese name for these islands, located further north from the island of Hokkaido.
Four of the archipelago's 56 islands were occupied by Russia during the Second World War and have been administered by Moscow since the end of the war in 1945.
The sovereignty dispute concerning these islands has been the reason behind Russia and Japan not having signed a peace treaty.
The territorial dispute remains unresolved for over 70 years and while efforts were on for negotiating a peace treaty, the Russian prime minister's visit was unacceptable for Japan and it did not contribute towards improving bilateral ties, said Kano.
The Foreign Minister urged Moscow to take constructive measures to bolster existing ties between the two nations.
Medvedev, during his visit to Iturup, inspected the construction of a school and houses and visited a factory for processing seafood, according to Russian state-owned agency TASS.
The Russian Prime Minister downplayed Tokyo's protest, claiming that the island was part of the Russian territory.
( With inputs from IANS )