"The Japanese side lodged a protest over the fact that if it is true, then it is incompatible with the basic position of [our] country," Suga told reporters.
Japan will continue negotiations on concluding a peace treaty and solving the territorial issue with Russia, Suga added.
On Tuesday, the Russian official ruled out that Russia could transfer the Kuril Islands to Japan for the sake of a peace treaty.
Oleg Morozov, a member of the Russian upper house's International Affairs Committee, believes that such protests only complicate the negotiation process on the peace treaty with Moscow.
"This is more than more than funny. The special representative of the president has the right to visit both in his personal and official capacity any place in the territory of Russia. There is not a single legal act that would exclude the Southern Kurils from the Russian territory… Japan complicates its relations with Russia by such actions. Territorial claims expressed in this form are ridiculous," Morozov told Sputnik.
Russian-Japanese relations have long been strained due the fact that the two nations never signed a permanent peace treaty after the end of World War II. The deal was never reached because of a disagreement over a group of four islands — Iturup, Kunashir, Shikotan and Habomai — that Russia has sovereignty over, but that are also claimed by Japan.
Since Russian President Vladimir Putin's visit to Japan in December 2016, the relationship between the two nations has been improving, with the two sides agreeing to develop joint projects on the disputed territories.
During the peace treaty talks with his Japanese counterpart in January, Russian Foreign Minister Sergey Lavrov stressed that the sides had confirmed their willingness to work on the basis of the 1956 declaration, "which means, first of all, the inalterability of… Japan’s complete recognition of… Russia’s sovereignty over all the islands of the South Kuril ridge."