Children are regularly shut in isolation rooms, tied to furniture or physically restrained by school staff, according to the country's leading advocacy group which blames inadequate teacher training.

Children with Disability Australia chief executive Stephanie Gotlib described the practices as "abuse", saying the organisation was fielding an increasing number of calls from parents distressed at the treatment of their children.

"We are hearing about incidents of restrictive practices more frequently, including restraints and seclusion," Ms Gotlib said.

"It is increasing and it's a clear reflection of a system which is inadequate in meeting the needs of students with a disability. Teachers are stretched to the max. Some of them don't have appropriate training. The system is in crisis."

Martial arts instructors have been used for "behaviour management" in Australian schools and children have been locked in "time out" rooms for extended periods, or physically restrained, according to a submission CDA made to the United Nations' Committee on the Rights of Persons with Disabilities in March.

Ms Gotlib said the incident involving the Canberra boy who was caged was far from isolated and she has repeatedly raised the issue with the Australian educational authorities.

University lecturer David Roy was shocked when he noticed bruising on his son Fraser's arm when he came home from class in the Newcastle region. Fraser, six, is non-verbal and has been diagnosed with autism and severe dyspraxia.

"We were horrified so we took him to the hospital to have it checked out and the staff said they could tell the bruising was caused by a hand," he said.

Mr Roy said staff failed to notice when Fraser escaped from the unit on two occasions and was found wandering unsupervised in the playground. He became increasingly alarmed by Fraser's deteriorating behaviour, including panic attacks and nightmares and parroting the word "retard" at home.

"We would say, 'How are you?' and he would say, 'retard'. That's not a word we use at home so the only place he could have heard it is in class," he said.

Mr Roy removed his son from the school and complained to the Department of Education, which found there was insufficient evidence to support the allegations.

Fraser is now being homeschooled, an option which Ms Gotlib believes is becoming more common for families who have lost trust in the education system.

"The Department of Education will argue that it's a safety issue and use that as justification for pinning a child down or isolating them in a room with no windows," she said.

"It is a form of abuse. Would teachers physically restrain a child without a disability? Would they isolate them? If I locked someone's child in a cupboard for a couple of hours or tied them to a chair, I would have the police on the doorstep."

Dr Sally Robinson, a research fellow at Southern Cross University, said the majority of staff working with children with disabilities were well-intentioned but often under-resourced.

"Children and young people with disability experience higher incidences of interpersonal harm at school compared to their peers, and across multiple life domains are abused at approximately three times the rate of children without disability," she said.

A Department of Education spokesman said it did not keep data on complaints specific to children with disabilities. He said teachers received appropriate training and only used restraints in certain instances.

"Any decision taken by staff to physically restrain a student should be exercised only in those circumstances where there is a real and immediate threat of injury to a person or serious damage to property and there is no other practical way of preventing the likely injury or damage," he said.

"Teachers are trained in classroom management and strategies to manage behaviour in the classroom."

He said the investigation into Mr Roy's initial complaint is complete but the department is looking into some new issues raised by the family.