"We have expressed our strong protest, saying that it is unacceptable," Suga told reporters at a briefing, adding that the protest was lodged through diplomatic channels on Thursday.
Earlier in the week, reports emerged that Russia had deployed the Bal mobile anti-ship missile system on Kunashir Island and installed the Bastion missile system on Iturup Island.
The Kuril Islands are the subject of the long-standing territorial dispute between Russia and Japan. Japan lays claims to Kunashir, Iturup, Shikotan islands and the Habomai group of islets. The territorial dispute has prevented Russia and Japan from signing a peace treaty after the World War II.