The Navy announced that the drill involves Navy, Air Force and Army forces, such as naval warships and aircraft, as well as Army and Marine Corp troops.
"Indeed, it's an exercise to guard our sovereignty and territory," Cheong Wa Dae spokesperson Ko Min-jung said at a press briefing.
She added that it's a regular training and asked media not to attach excessive "political" meaning to it.
The drills have been held twice a year, usually in June and December, to better fend off possible foreign infiltrations to the rocky outcroppings and the surrounding waters.
The timing of this year's practice has drawn keen public attention, with Seoul and Tokyo locked in an escalating trade fight.
Japan started imposing stricter export restrictions against South Korea in early July, a move apparently stemming from differences over wartime forced labor. Japan, which has made territorial claims to Dokdo, has protested the drills.
Tokyo claimed that South Korea is no longer trustworthy in terms of its handling of strategic, dual-use materials.
In a countermeasure, South Korea decided last week to terminate a major pact with Japan on exchanging military intelligence.
Ko said the Dokdo defense training is aimed at improving the military capability against potential threats from "all forces," not just Japan.
Asked about the schedule of this year's exercise, she added that weather conditions and "various other" factors were considered.
A Navy official earlier said the military formally named it "East Sea territory defense exercise" in consideration of its significance and size, a show of determination and resolve to defend the country's territories in the East Sea, including Dokdo.
Seoul's military drills immediately drew protest from Tokyo, which repeated its sovereignty over the islets.
In a protest lodged through a diplomatic channel, Tokyo expressed its "deep regret" over the drill and "strongly urged"
Seoul to stop the drill, saying the rocky islands, known as Takeshima in Japan, are "an integral part of the territory of Japan," according to Kyodo News Agency.
According to the Navy, the country's first Aegis-equipped destroyer, Sejong the Great, and nine other warships, along with 10 warplanes, including the F-15K, were deployed in the drills.
"Overall, the size of the armed forces doubled compared with previous levels," a Navy official said.
The Sejong the Great boasts the SPY-1D radar system capable of detecting and tracking 1,000 distant aerial targets simultaneously.
With the system, the warship has detected North Korea's missile launches, including its first long-range rocket test in April 2009.
It is also equipped with an advanced fire control system, due to which the vessel was selected as a Top Gun ship during the fire support training of the US-led multinational Rim of the Pacific exercise in 2010.
South Korea launched the Dokdo drills in 1986. Last year, the drills took place for two days in both June and December.
South Korea has maintained effective control of the nation's easternmost islets with a small police detachment since their liberation from Japanese colonial rule in 1945. Japan has persistently laid claim to Dokdo, drawing strong condemnation from the Seoul government.
Earlier this month, South Korea lodged a protest over Japan's marking of Dokdo as its territory on a map on the 2020 Tokyo Olympics website.
Seoul-Tokyo ties recently have plummeted to a fresh low after Japan dropped South Korea from the list of its trusted trading partners earlier this month following the announcement of tighter export curbs on July 4. In response, South Korea on Thursday announced its decision to terminate the military information-sharing pact with Japan. (Yonhap)