Claims that special needs children at Dunedin's Sara Cohen School have been hit, sat on and force-fed by staff, have been labelled false by several parents of pupils at the school.
The allegations are centred on several staff, including a teacher, at the Sara Cohen class for children with special needs at Concord School.
Ministry of Education special education director David Wales said the ministry was notified of parents' concerns in February.
''We immediately contacted the board of trustees in order to work alongside them to address the concerns and ensure the wellbeing of the students.''
The ministry employed education consultant Mike Corkery to conduct an investigation into the concerns raised by parents, and a limited statutory manager (LSM), Nicola Hornsey, was put in place in April to ensure the health and safety needs of pupils and staff, and to establish a proper complaints process, he said.
Police also investigated the school after a parent complained in February, but the investigation ended with no charges being laid.
There were allegations pupils in the class were being hit, sat on, pinched, force-fed, tackled to the ground and regularly put in a seclusion room by staff at the school.
Mr Wales confirmed one staff member had since resigned from the school and a second staff member had been suspended while the LSM carried out an employment investigation.
However, he could not confirm parent allegations the suspended staff member was a teacher in the classroom, or that the resigning staff member left because of the ''unfair'' suspension of the teacher.
A parent with a non-verbal autistic son at the school said the allegations were ''total c...''.
''I find it difficult to believe my son's teacher was harming him. If anything, she went above and beyond for our boy. She was awesome - such a good teacher. She was honestly, just the best.
''I don't believe the allegations are true.''
She believed the truth was being stretched to make incidents look worse than they really were
and was not aware of a seclusion room being used at the school.
Another parent supported the use of seclusion rooms.
''The ministry has outlined quite a clear policy on restraint and the use of seclusion rooms. That policy is really for across the board. It doesn't take special needs children into account.
''In a normal child, you can actually communicate with them, but in the case of autistic children, you're basically dealing with an 8-year-old toddler. You can't necessarily say sit down, because they're not going to listen to you.''
Another parent also believed the allegations were false, saying her 6-year-old son, who also had non-verbal autism, was at the centre of the force-feeding allegation.
He had sensory issues around food, and she had given his teacher permission to rub a little food on to his lips in a bid to expand the range of foods he would eat.
The teacher put a slice of banana to his lips to encourage him to eat it. But he refused it and the banana was taken away. The issue had been blown up into an allegation of a pupil being force-fed, the mother said.
She believed many of the injuries to pupils that had been recorded were inflicted by fellow pupils, not staff. A school incident report which detailed an injury to her son, inflicted by a fellow pupil, was ''completely inaccurate''.
''I witnessed the incident. But the report dismissed that I was even present. None of the allegations really line up.''
She also denied the existence of a seclusion room at the school.
Another parent said the allegations were put forward without the parents' knowledge.
''I didn't even know the nature of them until the police told me what was being said.
''There hadn't been any indication [from the school] that children were being abused.
''We were kept completely out of the picture for eight or more months. We've been stone-walled all year.''
One of the allegations was her 9-year-old non-verbal autistic daughter was being dragged around the classroom by her hair and made to sit at a table in restraints.
''I saw no sign of that. I'm pretty sure I would have known if that was happening. One of us [the mother or her ex-husband] would have noticed.
The parents believed the allegations were being made by other staff members at the school.
One of the parents said the lack of communication from school management had cast doubts as to whether she could really trust those looking after her son.
''It's caused us to look at sending him to another school.''
Mr Wales said some of the allegations made about the treatment of pupils in the school, including the previous use of seclusion, were very concerning ''but they are also subject to dispute''.
''The employment investigation is attempting to resolve these issues, so it would not be appropriate to comment further on them at this time.''
Ms Hornsey said allegations of misconduct had been made against several staff members, and she was aware some parents held certain views about the allegations.
However, she said it was her role as the legal employer conducting the employment investigation, to determine, on the balance of probabilities, what did or did not happen in the classroom.