South Korea, which controls the islets it calls Dokdo and Japan Takeshima, has been irate since Japan's Education Ministry this month showed them to be Japanese territory.
Han Seung-soo, the first South Korean prime minister to visit to the almost uninhabited islets, said, "Dokdo is the son of our country, and historically, geographically and legally belongs to us," Yonhap news agency reported.
Han, accompanied by South Korean culture and transportation ministers, set up a monument engraved with the words "Dokdo belongs to Korea," the report said.
Japan's Chief Cabinet Secretary Nobutaka Machimura said the issue should be handled in a calm manner, adding, "I don't think such action to stir up the differences is very appropriate," Kyodo news service reported.
The Japanese Education Ministry had said a teachers' handbook to be used from 2012 will treat the islets the same way as Japan's long-running claim over four islands under Russian control.
The ownership of the islets with numerous reefs and covering an area of 2.2 million square feet has long been under dispute.
The United States has stressed its policy of not interfering in the dispute.