Sibusiso Ndebele, South Africa's Correctional Services Minister, said an investigation had been opened into the latest allegations by Wits University's Justice Project.
A former G4S employee, who did not wish to be named, said he and his colleagues used electric shields because they were hopelessly outnumbered by dangerous prisoners.
"We use them sometimes because we are understaffed and we are expected to bring out the results and also to instil fear in the inmates," he told the BBC.
G4S has denied knowledge of any wrongdoing, saying that it had a "zero tolerance" approach to the excessive use of force.
"It is unfortunate that the media is pursuing a story based on unsubstantiated allegations from anonymous sources, disgruntled former employees and convicted criminals," said Andy Baker, the regional president for G4S Africa.
The allegations add to mounting problems for G4S, whose British chief executive resigned last week after questions were raised about its tagging of criminals.
During a year-long investigation, Ruth Hopkins, of the Wits Justice Project, spoke to former prison warders, members of the prison's medical team, members of the emergency security team and inmates.
British law firm Leigh Day said it was preparing a case against G4S on behalf of several inmates.