The joint operation by the Army, Air Force, Navy and Coast Guard was an effort to prepare for a situation in which foreign civilians trespass into territorial waters or attempt to illegally land on the islands in the sea between South Korea and Japan, the Yonhap News Agency reported.
It is called the Sea of Japan in Japan and the East Sea in South Korea.
"The exercise was carried out under the scenario in which the Coast Guard took a leading role in repelling foreign civilians invading territorial waters near Dokdo or trying to land on Dokdo," Col. Lee Bung-woo, the Joint Chiefs of Staff spokesman, said. "The military provided support for the Coast Guard during the operation."
After the drill, the South Korean Navy was expected to conduct its own training in the sea through Monday, Yonhap reported.
South Korea has maintained the territory is Korean based on history, geography and under international law. A small Korean police unit is stationed on the islands.
The Japanese Parliament condemned what it called Korea's "illegal occupations" of the territory known as Dokdo in Korean and Takemisha in Japanese.