A North Korean senior colonel, whose name has been withheld, defected in 2015 after working at the North's reconnaissance bureau tasked with carrying out espionage missions against the South, the ministry said.
"(The North Korean military official's defection) is a fact, but we cannot make public detailed information (about him)," Moon Sang-gyun, a ministry spokesman, said at a regular press briefing.
A source familiar to North Korean affairs said that the officer is viewed as an elite among North Koreans who have defected to the South.
"He is believed to have stated details about the bureau's operations against South Korea to authorities here," the source said.
South Korea's spy agency said last year that since taking power in late 2011, North Korean leader Kim Jong-un has had more than 70 senior officials executed in an effort to tighten his grip on the communist regime.
A number of North Korea's working-level officials based in foreign nations have sought asylum apparently to avoid Kim's so-called reign of terror, according to various sources.
The North's Reconnaissance General Bureau deals with intelligence gathering and espionage operations in foreign countries, and is also responsible for cyberwarfare. The bureau is known to be behind Pyongyang's alleged cyberattack on Sony Pictures Entertainment in 2014.
Kim Yong-chol, a new party secretary handling inter-Korean affairs, had served as the head of the bureau since 2009.
In a separate case, a North Korean diplomat stationed in an African country and his family members defected to South Korea in May last year, said another source having knowledge about North Korea.
Last week, a group of 13 North Koreans who used to work at an overseas restaurant en masse defected to South Korea, the first mass defection since 2011. North Korean-run restaurants in foreign nations have served as a source of hard currency for Pyongyang.
The latest case came as the U.N. Security Council and major countries have slapped tougher sanctions on North Korea for its January nuclear test and long-range rocket launch in February.
South Korea's intelligence agency and other government organizations, meanwhile, have started processing the defectors to find out the motivation behind their action, according to a government source.
There are more than 28,000 North Korean defectors in South Korea, with some 1,280 North Koreans entering the South last year, according to Seoul's unification ministry. (Yonhap)