The dispute is an emotive one, and sparked fresh protests in Seoul
South Korea says it is to recall its envoy to Japan in the latest flare-up of tensions over disputed islands.
The foreign ministry said Japan had reasserted its claim to the islands, which are under South Korean control in waters between the Asian neighbours.
The fresh claim to Japanese ownership of the islands - known as Dokdo in Korea and Takeshima in Japan - was reportedly made in a book for teachers.
The islands sit in rich fishing grounds which may also contain gas reserves.
Ambassador Kwon Chul-hyun will return home temporarily after lodging a strong protest with Japan's foreign ministry, the Seoul foreign ministry said.
Japan's ambassador to Seoul, Toshinori Shigeie, would also be summoned, the ministry said.
South Korean President Lee Myung-bak expressed "deep disappointment and regret" about Tokyo's fresh claim of sovereignty over the islands, which South Korea says is made in a teacher's guide to middle-school textbooks.
President Lee has sought to cultivate better ties with Tokyo. In April he held the first full summit meeting between the two in three years.
Meanwhile in Tokyo, government spokesman Nobutaka Machimura said his government had been cautious about the phrasing of the guidelines, and called for calm.
"Needless to say, South Korea is an important neighbour for Japan," he said.
"We want to avoid a situation where Japan-South Korea relations are influenced by each and every issue, and I hope both sides will calmly respond."
Protests were seen at the Japanese embassy and elsewhere in Seoul, with riot police reportedly deployed in response.
South Korea and Japan both insist they have the stronger historical claim to the islands, going back hundreds of years.
The recent dispute centres on whether they were covered by Japan's renunciation of sovereignty over its occupied territories following its defeat in World War II.
South Korea stations a small unit of maritime police on the rugged and treeless islands, which cover a total area of 18.7 hectares (46 acres).