The Unification Ministry said Thae Yong-Ho - the number-two at the North's mission in London - had defected together with his family and they were now in the South Korean capital.
"They are under government protection and are going through necessary procedures with related institutions," ministry spokesman Jeong Joon-Hee told reporters.
Jeong declined to reveal Thae's defection route, citing the diplomatic sensitivities involved for the concerned countries.
"On his reasons for defection, Minister Thae cited disgust with (North Korean leader) Kim Jong-Un's regime, admiration for South Korea's free, democratic system and the future of his family," Jeong said.
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The last such case was that of the North Korean ambassador to Egypt who defected to the United States in 1997.
South Korea' JoongAng Ilbo newspaper, which first reported Thae's defection yesterday, said he had been under pressure from Pyongyang to combat growing international criticism of North Korea's human rights record.
North Korean defectors have been making headlines recently, largely due to an unusual group defection in April by a dozen waitresses and their manager who were working at a North Korean-run restaurant in China.
The Unification Ministry said Thae's defection reflected the loss of faith among North Korea's elite in Kim Jong-Un's leadership.
"Awareness that the North Korean regime has reached its limit is spreading and the solidarity of its ruling class is weakening," Jeong said.
Thae was believed to have worked at the embassy in London for 10 years, with one of his main tasks being to counter the image of North Korea as a nuclear pariah state and notorious human rights abuser.
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