Correctional Services said that “matters are under control” at Johannesburg’s Sun City Prison on Wed.
Police say that if the father of the Alexandra boy who disappeared feels that his rights were violated, he should open a case with the police.
Mzwandile Jele, 37, claims that police tortured him when they took him in for questioning in connection with his son's disappearance on Sunday.
His son, Lesley Mhlanga, 3, disappeared while playing with friends outside his Alexandra home three weeks ago.
On Sunday, police took Jele in for questioning regarding Lesley's disappearance.
He claims police tortured him into confessing that he had kidnapped his son.
"I'm very sad about what happened. My hands were handcuffed behind my back and I was pressed down on the floor while a refuse bag was put over my face," Jele said.
Sergeant Sanku Tsunke said: "The claims this man is making are very serious. He should open a case."
Jele's ex-lover, Selina Khumalo, 47, was arrested in connection with the boy's kidnapping.
Lesley was allegedly kidnapped by a woman who promised him sweets.
The boy's mother, Neria Mhlanga, said that whoever has her child must bring him back unharmed.
Tsunke said that there was still no new evidence in the case.