The foreign ministry summoned Japanese Ambassador Koro Bessho to formally convey its protest over a section in Japan's newly released foreign policy report "Diplomatic Bluebook 2014".
The report, drafted every year by the Japanese foreign ministry, identified the disputed islets -- known as Dokdo in Korean and Takeshima in Japanese -- as Japanese territory.
It also vowed intensified efforts to have the dispute over the South Korean-controlled islets settled by international law.
Japan's repeated claim will not only "severely" damage bilateral ties, but threaten peace and security in Northeast Asia, the statement said.
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Relations between Tokyo and Seoul are currently at their lowest ebb for years, mired in emotive disputes linked to Japan's 1910-45 colonial rule, including the islet dispute.
The foreign ministry also warned Japan to scrap plans to revise school textbooks to strengthen its historical claim to the rocky outcrops in the Sea of Japan (East Sea).
"The path for mending South Korea-Japan ties will become longer if the Japanese government continues its provocations regarding Dokdo," it said.
Three weeks ago, Japanese Prime Minister Shinzo Abe and South Korean President Park Geun-Hye met in The Hague in a summit hosted by Obama.
Tokyo said the meeting had provided an opportunity for Abe and Park to build a rapport, but Seoul's verdict was far cooler.