The department confirmed the attack and said it had implemented countermeasures to isolate the affected system. Those measures included software patches from Microsoft, the agency said.
Several entities in South Africa have been compromised by hackers who exploited a security vulnerability in Microsoft's SharePoint servers, according to Eye Security, the cybersecurity company that identified an early wave of attacks last week.
Hackers breached about 400 government agencies, corporations and other groups around the world, although the number could be a lot higher, the Dutch company said.
Most of the victims are in the US, followed by Mauritius, Jordan, South Africa and the Netherlands, it added. Microsoft warned earlier this month that hackers were actively targeting customers who manage SharePoint on their own networks, as opposed to being hosted and managed on the cloud.