Durban - A bus driver has been arrested for allegedly raping a 13-year-old autistic girl from a special needs school, despite the KwaZulu-Natal education department saying previous claims of sexual and physical abuse there had been dealt with.An investigation into the Inkanyiso Special School in Vryheid started in 2016, after staff members wrote to education advocacy group Equal Education, claiming children there were being subjected to rampant abuse.The allegations were addressed, department spokesperson Muzi Mahlambi said.Now the school is back in the spotlight following the arrest of the driver, who allegedly raped the teenager at the back of the bus on March 8.Speaking to News24, the girl's distraught mother said: "The child doesn't want to back to school anymore and is reliving the trauma of the rape."The woman, who may not be named to protect the identity of her daughter, said she would not rest until she got justice for her child.Her daughter was walking home from school when the driver picked her up. He waited until she was the only passenger left before he allegedly took her to the back of the bus and raped her.Police arrested the 46-year-old driver man.READ: Hostel hell for disabled children'Flashback memories'National Prosecuting Authority spokesperson Natasha Kara said he had appeared in court and was released on R1 500 bail, on condition that he did not go near the school. He would be back in court on April 24.The mother said she had received threatening telephone calls, warning her not to pursue the matter."Firstly, I was victimised, in that my innocent child was raped. Now I am also being threatened. No matter what they do, they won't get peace," she vowed.She was considering taking her daughter out of the school."She is frightened. She keeps getting flashback memories. If you speak to her, she just jumps in fear. She is also not speaking. Normally she speaks a lot."According to a source, staff members were not informed about the rape until Friday, March 17."Nothing was being said about it and it was a blatant cover-up," said the source.News24 has sent questions to the principal, who has not responded.Mahlambi said the department was not aware of the latest allegations, but said it would help during court proceedings as a friend of the court.Appalling conditionsThey would ask for a report from the district office and determine what had been done so far. The department would launch internal action against the driver. Preying on innocent children, especially special needs pupils, was reprehensible, he said.In 2015, City Press reported that children at the school were being forced to eat on the floor and lived in appalling conditions at its hostel. A physically handicapped child was left unattended on the floor, according to video footage.The publication reported that school funds were being mismanaged and that pupils were physically and sexually abused.Aggrieved teachers were still awaiting the findings of a report commissioned by the department into these allegations.The report was sent to the South African Human Rights Commission and Equal Education’s law centre in July 2016.Mahlambi said the allegations against the school had been resolved."They are processes and mechanisms are in place to deal with special school matters," he said.