The Shimane Prefectural Government on Sunday marked its fourth "Takeshima Day" promoting Japan's claim to the disputed group of South Korean-controlled islets in the Sea of Japan.
There was no major disruption except for a skirmish between several South Korean protesters and police officers who tried to stop outdoor protests.
The South Korean government reacted sharply to the events in Matsue.
"The government expresses deep regrets that Japan's Shimane Prefecture had an event to mark 'Dokdo Day' despite our repeated request (not to do so)," South Korean Foreign Ministry spokesman Moon Tae Young said in a statement quoted by Yonhap News Agency.
Koreans call the rocky outcroppings Dokdo.
The Foreign Ministry did not send an official from Tokyo for the fourth consecutive year despite a request from the prefectural government.
Upper House member Eriko Yamatani of the ruling Liberal Democratic Party gave a speech at the ceremony, the first Diet member to take part.