Tension over the contested islets was heightened when the Tokyo central government sent a senior Cabinet official to the annual "Dokdo Day" event, the Yonhap News Agency reported.
Japan's Shimane prefecture, which claims administrative control over the islands, has held the event every Feb. 22 since 2006 to emphasize its claims, but this was the first year a member of the central government attended.
In protest, South Korea "urged Japan to abolish ordinances about the designation of the Dokdo day and to immediately stop unjustifiable territorial claims to Dokdo," South Korean Foreign Ministry spokesman Cho Tai-young said in a statement.
The government vowed it would make "strong responses" to any provocative action by Japan.
The decision to send Aiko Shimajiri, a parliamentary secretary with the Cabinet Office, to the event was criticized as a "grave criminal act" by Kim Kwan-yong, governor of North Gyeongsang province, which administers the islands for South Korea. They are called the Takeshima islands in Japan.
A group of about 100 people demonstrated in front of the Japanese Embassy in Seoul and delivered a letter to the embassy asking Japan to be "a true neighbor instead of seeking an aggressive attitude."