It was infected with a malicious code when an unsuspecting staff member opened an e-mail at the Hana Centre in North Gyeongsang province.
South Korea has denied the allegation, saying its warship used an optical camera while rescuing a North Korean fishing boat in distress.
In order to prevent such leaks in the future, the government is working to separate the computers storing confidential data at the 25 resettlement facilities across the country run by the Hana Center, so the systems tasked with storing information about North Korean defectors will not be connected to the internet, making it hard for cybercriminals to get their hands on them. The Unification Ministry was, however, fairly confident a file containing personal information was stolen in the incident.
The North is seen as trying to drive a wedge between the US and South Korea so that it can draw more support from the South's administration of President Moon Jae-in, which wants to maintain conciliatory mood between the two Koreas. "The file was confirmed to have been leaked".
The ministry added that this was the first ever large-scale leak of such kind involving North Korean defectors.
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A regional office of the Hana resettlement center said it has been notifying affected defectors after discovering last week that one of its computers had been breached sometime around November.
The defector community expressed concern about the information breach. The official did not say if the North Korean government is suspected of carrying out the attack.
The widespread leaking of sensitive information was especially damaging for the defectors, who mostly live low-profile lives in fear of revenge from the North's communist regime.
In October, cybersecurity firm FireEye accused the North Korean government of using a state-sponsored hacking group to steal more than $100 million in "particularly aggressive" attacks on global banks.
South Korea's police is investigating the apparent cyberattack to find out who is behind it and whether the illegally obtained data were misused.