Correctional Services Minister Sibusiso Ndebele was responding to a Mail & Guardian article by the Wits Justice Project that reported inmates in the maximum security centre were forcibly injected with anti-psychotic medication and electro-shocked to "subdue and control them".
Ndebele described the alleged acts as inhumane.
"The department views these allegations … in a very serious light. We will leave no stone unturned in this investigation," he said in a statement.
The probe would be led by Gauteng regional commissioner Zacharia Modise, who had been managing the prison since October 9.
The department took over management of the formerly privately-run prison outside Bloemfontein.
It said that private security company G4S had lost control of the facility.
One of the main reasons for the intervention, it said, was a concern for the safety of inmates and staff.
G4S had dismissed 330 staff affiliated to the Police and Prisons Civil Rights Union after they refused to return to work at the prison following a strike.
During the strike the facility, which houses nearly 2000 inmates, was run with limited staff.
A riot broke out, various staff members were stabbed, and inmates took a woman warder hostage for 13 hours.
The police's special task force rescued her unharmed. The four inmates who held her hostage were arrested. – Sapa