Kagiso police kept a mutilated boy with them for an undisclosed time because "they are not allowed to transport injured people".
A member of the public, Snega Konyana, eventually took the boy to Leratong Hospital in his car.
The boy, whose age is estimated to be between two and four, was found with his private parts mutilated.
Konyana said the boy was sitting on a bench in the police station. He opened the boy's pants and was shocked by what he saw.
"His private parts were gone," Konyana said.
Police spokesman Solomon Sibiya said there were restrictive policies that prevented them from transporting injured people.
"But we called the police [sic] and while we were waiting a member of the public volunteered to take the boy to the hospital," he said.
Sibiya said they were not negligent in dealing with the matter.
Provincial police spokesman Lungelo Dlamini said: "There are restrictions but they act as guidelines. The police should have looked at the circumstances and used their discretion."
He said the police would conduct an investigation and disciplinary steps would be taken if necessary.
Lydia Hlahane, who carried the boy to the police station, said she did not realise that he was badly injured.
"He could not speak when we asked him what happened. I only realised the extent of his injury at the police station," she said.
This is the second time that the police have allegedly dragged their feet in helping the public in recent days.
Last Sunday seven-year-old Gofaone Tyatya of the Zandspruit informal settlement went missing while playing outside her house. The family complained that the police did not react swiftly.
Her bruised and blood-spattered body was found by a security guard when he was returning home after work.
She had been raped.