Patricia and Richard Alford removed their daughter, Georgia, from the school when they received an anonymous letter claiming she was verbally abused and mocked by staff at Jarrow School's Post 11 Autistic Unit.
Georgia, who suffers from learning difficulties and has communication problems, has been unable to confirm the claims because of her condition.
Mr Alford, 51, from West Boldon, Tyne and Wear, said: "Whichever way you look at it, this is a problem. Either the letter has been written by a disgruntled teacher, or there is a basis to the allegations.
"We have been told the Autistic Society will be part of the investigation, which is what we have been pushing for."
Georgia, Patricia and Richard Alford
The anonymous author of the letter also said other children at the school had been called names and pushed by teachers.
Speaking at the time of receiving the letter in July, Mrs Alford, 54, a nurse, said: "I don't blame the person for sending the letter - but it was horrific to receive it.
"We have pulled Georgia out of the school. We feel other parents should be made aware about these claims."
Mr Alford, a former banker and full-time carer for Georgia, said: "To read that she had been called a fat f**k is atrocious.
"I could almost understand if it was another pupil but if it's a member of staff, then they shouldn't be doing their job.
"They should be calling their professionalism into question if they are saying things like that to children.
"You have to be able to have full trust in the people caring for your daughter.
"This is a safeguarding issue. The hardest thing is that, due to her condition, we cant just ask Georgia what has happened and find out from her."
South Tyneside Council is now looking at the welfare and safety of students at Jarrow School's Post 11 Autistic Unit.
This independent probe into the allegations is taking place following a campaign by Mr and Mrs Alford, who were not satisfied by an internal investigation by the school.
Mr Alford added: "We had a meeting with staff at the school, which was also attended by Peter Cutts, South Tyneside Council's head of education, in which he told us there would be an independent panel set up to look at our concerns.
"We do feel as if some good has come out of this."
A spokeswoman for the council said: "The council takes all matters of safeguarding very seriously and, with support from the school, is commissioning an independent review of the Post-11 unit, including the quality of the provision and children's welfare and safety.
"The school has completed its internal inquiries into anonymous allegations made and has reported its findings back to the parents."
Jarrow School was rated good in its latest Ofsted inspection with inspectors rating both behaviour and safety of pupils and leadership and management as outstanding.