Thae Yong-ho, formerly North Korea's deputy ambassador in Britain, is understood to have abandoned his duties earlier this month.
He then travelled to Seoul along with his wife and children. "They are under government protection and are going through necessary procedures with related institutions," said a South Korean government spokesman.
"On his reasons for defection, Minister Thae cited disgust with Kim Jong-un's regime, admiration for South Korea's free, democratic system and the future of his family,"
North Korea and Britain established full diplomatic relations in 2000 and both countries have embassies in one another’s capitals. Six diplomats serve at the North Korean mission in Ealing, west London, according to the latest version of the London Diplomatic List.
Mr Thae's official title is given as "minister" at the embassy and the Diplomatic List places him in second place of seniority below Hak Bong-hyon, the ambassador. There are four other diplomats with various functions, including two “counsellors” specialising in “maritime affairs”.
Over the years, many officials from Pyongyang have defected to South Korea. But defections from North Korea's diplomatic corps, which is carefully vetted for ideological purity, are extremely rare.
John Nilsson-Wright, a North Korea expert at Chatham House, said that Mr Thae's defection could be extremely valuable for Western and South Korean intelligence agencies.
He told the BBC: "London has always been an important diplomatic priority for [North Korea] given the amount of personnel stationed there and the considerable resources devoted by the regime to maintaining its presence there. The intelligence benefits to the UK and its allies from such a defection are likely to prove valuable."
Starved of funds from Pyongyang and representing one of the most isolated regimes in the world, North Korea’s diplomats have a low profile in London. In 2014, two of these envoys visited a barber near their embassy to complain about a poster of Kim Jong-un, the North Korean dictator, with the caption “Bad Hair Day”.
Two North Korean diplomats also escorted Mr Kim’s elder brother, Jong-chul, to an Eric Clapton concert in the Royal Albert Hall in 2015.
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