Dozens of riot police were deployed to protect Japan's embassy in Seoul, where protesters burned Japanese flags and defaced photos of Ambassador Toshiyuki Takano.
Mr. Takano sparked anger among South Koreans when he told reporters Wednesday that a handful of tiny islets between the two countries are "historically and legally Japan's territory."
South Korea and Japan have disputed ownership of the uninhabited islets since the end of the World War II. South Korea calls them Dokdo, while Japan calls them Takeshima. Both countries cite historical documents they say prove their respective ownership.
Ambassador Takano's comment came soon after the assembly in the Japanese prefecture of Shimane sparked Korean anger by putting forward a bill to commemorate "Takeshima Day."
A senior Japanese diplomat was summoned to the South Korean Foreign Ministry Thursday. Lee Jung-il, of the Foreign Ministry's Asia-Pacific Affairs Division, says South Korean officials expressed displeasure at Mr. Takano's comment.
"We pointed out that it is very embarrassing for the ambassador stationed here [to speak] about some subtle issues in a way that instigates our national sentiment," he said.
A Japanese embassy official, who asked to not be identified, says the ambassador does not regret his remark. He said most Japanese people hold the opinion the islands are under Tokyo's sovereignty.
The controversy comes at an inconvenient time for the two countries, which are trying to cooperate closely to bring North Korea back to multilateral negotiations on ending its nuclear weapons programs.
Authorities in Tokyo and Seoul say they are committed to a calm and peaceful resolution to the island dispute. They say the disagreement over the islands will be treated as an entirely separate affair from the nuclear talks.