Children were allegedly locked in cage-like structures at a Victorian special school and restrained with straps at another, triggering separate investigations by the Education Department.
A consultancy hired by the department is investigating practices at Bendigo Special Developmental School to determine whether there is "a risk of danger or risk of inappropriate treatment" for students.
A separate probe by an independent education consultant is examining complaints raised by parents at Monash Special Developmental School.
The investigations follow revelations that a cage was built in Canberra classroom for a 10-year-old autistic boy.
Disability advocate Julie Phillips has received reports from former staff, parents and visitors at Bendigo Special Developmental School that children were placed in a cage-like structure in a classroom up until 2011.
She suspects the cage in the classroom was dismantled in 2013 but said other cage-like structures in the school's playground still exist.
Ms Phillips said staff at the school were trained by martial arts experts and used pressure points to move students.
"Unfortunately, staff and parents who have spoken out against these practices at both these schools have been subjected to significant victimisation," she said.
Ms Phillip said she was concerned the department's investigation would protect staff accused of abusive practices ahead of students.
"This has been reflected in their refusal to investigate abuses that occurred in the past, no matter how severe."
Jessie Allen pulled her son Justin out of Bendigo Special Developmental school in 2015 after he became withdrawn and unhappy.
He came home with bruises in 2012 and the following year told his mum there was a cage-like structure in the classroom and outside.
"He assumed they were for puppy dogs and then realised they were for children."
He recently told his mother that he was locked in a structure that "looked like a cubby house but with no windows" in the playground.
"He has to live with this for the rest of his life," she said.
Bendigo Special Developmental School principal Julie Hommelhoff said there were no cages at the school.
"I fully welcome this independent investigation and the school is fully co-operating with this important process."
The department said it commissioned an investigation into Bendigo Special Developmental School following concerns by disability advocates.
"A comprehensive investigation into practices at Bendigo Special Developmental School is under way," a spokeswoman said. " The investigation will determine whether there is a risk of danger or risk of inappropriate treatment of students attending Bendigo SDS."
Monash Special Developmental School, which caters for disabled students aged from 2.8 years to 18, is being investigated following complaints from two parents, including Tracey Hayes. There are no allegations of cage-like structures at the school.
Ms Hayes complained to the department after a teacher sent her photos of her twin sons being restrained with straps in a stroller and chairs at the school.
"The photos did not lie," she said. "I'm really distressed about it still. It has affected myself and my boys."
Her children, who have autism, left the Wheelers Hill school in 2014. They now attend a mainstream state school, where they are not restrained, she said.
Monash Special Developmental School principal Helen McCoy said the school had "fully co-operated with this review which has mainly examined historic practices".
The Andrews government recently appointed a "principal practice leader" who will report to the Senior Practitioner to reduce the use of restrictive practices in schools.
Under a new state government initiative, teachers will have to report every time they restrain or seclude a child to control their behaviour.