Parents have told an IHC survey their disabled children are being bullied at school, many are not getting enough support, and some have been illegally blocked from enrolling altogether.
The organisation, which provides support and advocacy for children with disabilities, said the results were grim and showed that schools were struggling to get enough resources to work with children with special learning needs.
It said nearly 300 parents and 140 educators responded to the survey last year.
Seventy-three percent of the parents who responded said their child did not go to school full-time, and 27 percent said the past five years a school had refused to enrol their child or put conditions on their attendance.
Fifty-eight percent said their disabled child had been bullied in the past five years and only 43 percent believed their child received enough support to allow them to thrive at school.
However, the figures showed some improvements since the IHC ran a similar survey in 2014.
The percentage of parents saying their children could not attend full-time due to a lack of teacher aide hours had dropped from 32 percent in 2014 to 23 percent last year and the percentage saying their child's teacher did not have the right skills to work with disabled children dropped from 72 percent to 52 percent.
Among education professionals, 44 percent said teachers did not have the right skills, an improvement since 2014 when the figure was 64 percent.
The director of advocacy at IHC, Trish Grant, said that was encouraging but still not good enough.
"Actually you only get a 50 percent chance, according to our survey, of having a teacher who knows how to teach you. Now that's not good by anyone's standards," she said.
Overall, Grant said the survey results were not good.
"It still paints a very grim picture of what disabled children are experiencing, of what families are experiencing and what schools are experiencing. A lot of stress out there."
Grant said the survey showed schools did not have the resources they needed to provide learning support and she was especially worried that some were turning away disabled children.
"That's a very high indicator of a system under pressure," she said.
The president of the Principals' Federation, Perry Rush, said he was saddened that some schools were refusing to enrol children with special learning needs because inclusion was an important aspect of the school system.
However, he warned that there were limits to what schools could do.
"It's an indication of an inclusion policy that isn't sufficiently met by the appropriate resourcing," he said.
"What we're seeing here is principals doing their best to try and draw a line that works, and works as much as possible for the students in their care and also for the resourcing they're given to do their job."
Rush said teachers were better prepared to provide learning support but they needed more specialists who could work one-on-one with students with special needs including severe behavioural difficulties.
"I don't think that we have sufficiently explored the impact of the policy of inclusion on schooling. I know from my conversations with colleagues that there's a good deal of concern around the need to see greater resourcing to meet the needs of every student in our care."
Rush said funding for learning support had increased in recent years, including the creation of new learning support coordinator positions, but schools were struggling to see the benefits of those improvements.