State Information Technology Agency (Sita), which hosts all of the government's websites, said that last week the hackers accessed information relating to crimes posted by some 15,000 whistleblowers and complainants.
"Most of the information was submitted anonymously... We are concerned because there is information where people have given further details" of crimes, Daniel Mashao, Sita's divisional manager, was quoted as saying by SAPA news agency.
The hackers then posted the information onto a public website.
The hacker "DomainerAnon" claimed responsibility for the cyber attack in a tweet late last week, saying it was linked to last year's killing by police of 34 striking workers at the Marikana platinum mine operated by Lonmin.
Police have launched an investigation into the breach, which only discovered yesterday.