Almost 1,000 North Korean defectors have had their personal data leaked after a computer at a South Korean resettlement centre was hacked, the unification ministry said.
A personal computer at the state-run centre was found to have been "infected with a malicious code".
The ministry said this is thought to be the first large-scale information leak involving North Korean defectors.
The hackers' identity and the origin of the cyber attack is not yet confirmed.
North Korean state media has also often threatened to silence defectors in the South who make derogatory statements about the regime.
However, the government in the South has not pointed the finger at North Korea this time, although many cyber-security experts been warning of the increasing sophistication of hackers from the North.
One of the most high profile hacks linked to North Korea in recent years targeted Sony's entertainment business in 2014 - wiping out massive amounts of data and leading to the online distribution of emails, and sensitive personal data.
Are defectors' families in danger?
Some 997 North Korean defectors have now been informed that their names, birth dates and addresses have been leaked but it is not clear what impact this will have.
Analysts say there are some concerns that the leak could endanger the families of the defectors that still remain in North Korea.
On 19 December, the unification ministry became aware of the hack after they found a malicious program installed on a desktop at a resettlement centre - also known as Hana centres - in North Gyeongsang province.
These are the institutes which the South Korean government run to help the thousands of defectors that have come from North Korea adjust to life in the South.
The ministry said that no computers at other Hana centres across the country had been hacked.
One expert on North Korean cyberwarfare, Simon Choi, believes that this might not be the first time a Hana centre has been hacked.
"[There is a North Korean hacking] group [that] mainly targets [the] North Korean defector community... we are aware that [this group] tried to hack a Hana centre last year," he told the BBC.
However, he added that it was not yet clear if any North Korean groups were responsible for the latest attack.
Investigations by the ministry and the police are currently ongoing, with the ministry saying it would "do its best to prevent such an incident from happening again".