A 13-year-old boy with Down syndrome was raped in the classroom of his special needs school by a staff member, it has been alleged.

The boy told his mother he was locked in the classroom earlier this month at a school east of Johannesburg, South Africa.

The boy’s mother, who has not been named, said her son was acting strangely when she picked him up from school and she noticed a strange smell.

Speaking to local publication Sowetan Live, she said: “His eyes were red as if he was crying and when we stepped into the vehicle, I noticed a smell emanating from him. As if he didn’t wipe himself properly after using the toilet.”

She said she had spent over an hour looking for her son at the East Rand school on Aug. 5.

“I was frantic when I didn’t find him where I usually pick him up,” she said.

The mother, along with a teacher and the vice principal of the school, walked around the school calling out his name to no response.

It was then that the mother claimed a “general worker” at the school came running in their direction, hesitating when he saw the teachers.

She recounted an exchange in which the teacher explained they were looking for a missing boy.

“He offered to help us find him, saying that my son was probably asleep in one of the classrooms,” the mother recalled.

“He went to one classroom and unlocked it. It was strange that my son came out immediately — not like someone who was asleep — but like someone who had been up and was waiting for the door to be opened.”

But she didn’t think much of it due to the relief of finding her son.

Police spokesperson Capt. Ramothaki Maqwabe confirmed that a rape case was being investigated.

However, the boy’s distressed mother said the principal of the school told her that her son would have to spend three months away from school until investigations were concluded.

She believes this fails to deal with the matter as the alleged perpetrator has been allowed to return to work.

“What upset me was the school’s decision not to suspend the man who did this but told me to keep my son at home until the investigation was finalized,” she explained.

“But I reported it to the department [of education] and it intervened. I was then told that my son could return and the worker would be limited to the school’s garden and not around the classrooms. What more do the police need? We gave them a statement and they know exactly who needs to be arrested,” she said.

The mother said doctors confirmed the boy was raped.

Education spokesperson Steve Mabona said the worker had been suspended immediately after the incident and that he will appear in a disciplinary process in due course.

He said the school followed the correct procedure in dealing with the incident, reported the matter to the police and provided the child and his mother with counseling.

“We will request the police to escalate this sensitive case to the province for necessary attention,” he added.

No arrests have so far been made.