A 5-year-old boy was raped at Shongwe Hospital in Nkomazi, Mpumalanga, allegedly by a 12-year-old boy, provincial police spokesperson Colonel Donald Mdhluli said on Monday.
Mdhluli told News24 that the boy was raped on 13 November, but he would not reveal details of the incident.
He said once the investigation was concluded, a forensic report would be handed to the provincial director of public prosecutions for a prosecution decision.
"The forensic investigation report is the one that will reveal everything," Mdhluli said.
"There is no new development [in] the investigation at this stage. Both the children are minors. Cases like this one also involve social workers and other stakeholders. We need to give them space. It is not the SAPS alone that is investigating."
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No arrests have been made.
Spokesperson for the provincial health department, Dumisani Malamule, said the department was also conducting an internal investigation, but declined to reveal more details.
"We are busy checking what transpired. We cannot say what happened at this stage."
Malamule did not say whether the two boys were patients at the time that the incident occurred.