IturupPutin sampled fish roe on the disputed island.
It is his first visit to the chain, asserting possession over land Japan still claims.
Soviet forces seized the islands in 1945, the reason Russia and Japan never signed a peace treaty.
Foreign Minister Toshimitsu Motegi lodged a formal protest, with no legal recourse to reverse the visit.
Sources: 朝日新聞デジタル, BBC, News18, B92, The Straits Times