The classified data was leaked through a personal computer. It was infected with a malicious code when an unsuspecting staff member opened a mail at the Hana Centre in the North Gyeongsang Province.
There are 25 such centres across the country which provide support for the roughly 30,000 North Korean defectors who live in the country.
After confirming the hack last week, authorities conducted an emergency inspection of all computers at Hana Centres but no other leaks were found.
"We apologise to defectors from the North. We will make utmost efforts to protect their personal information and prevent any recurrence of such an incident", the ministry said in a statement.
North Korea's state media have threatened to silence defectors who actively engage in anti-Pyongyang activities such as launching leaflets to the North by balloons.
Yi Han-yong, a nephew of Song Hye Rim -- the first wife of late North Korean leader Kim Jong Il -- was shot to death outside his house in Bundang, south of Seoul, in 1997.
His assassination by two attackers, who were never caught, followed the publication of his tell-all book about the private life of the Kims.
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