South Korea's coast guard is leading military exercises near islands also claimed by Japan, amid ongoing tension over the territorial row.
The operation near islands known as Dokdo in South Korea and Takeshima in Japan also involves the army, navy and airforce, South Korean media said.
Tensions have risen since a visit to the islands by South Korea's leader.
Japan wants international arbitration over the islands, but South Korea has rejected the proposal.
Last month Japan briefly recalled its ambassador to Seoul in protest over a surprise visit to the islands by President Lee Myung-bak.
South Korea, which controls the islands, has maintained a small police force there since 1954.
"The exercise is carried out under the scenario in which coast guard takes a leading role in repelling foreign civilians invading territorial waters near Dokdo or trying to land on Dokdo," Col Lee Boong-woo was reported as saying by Yonhap news agency.
South Korea has decided to exclude exercises that involve landing on the islands in a move that is ''mindful'' of the diplomatic row with Japan, the Yonhap report said.
Previous exercises had involved marines landing on the island, it added.
The row between the two countries over the islands - which are roughly equidistant from both - has flared sporadically in recent years, amid lingering antipathy over historical issues.
Mr Lee's visit on 10 August - the first by a South Korean president - was followed by relay swim by 40 South Koreans to the islands to mark the anniversary of the country's liberation from Japan in 1945.
Japan is also embroiled in another territorial row with China in the East China Sea. Both countries claim islands known as Senkaku in Japan and Diaoyu in China.
Reports suggest the Japanese government has reached a deal to buy the islands from their private Japanese owner, potentially further raising tensions with China.
Leaders of all three nations are due at the Apec (Asia-Pacific Economic Cooperation) summit in Vladivostock this weekend.
But Japanese Foreign Minister Koichiro Gemba said Prime Minister Yoshihiko Noda was unlikely to hold bilateral meetings with Chinese and South Korean counterparts
"I think it will be better not to make (meetings) official," Kyodo news agency quoted him as saying.