Disability and race relations matters were the most common complaints made to Human Rights Commission, the report said.
Mrs Collins said some mainstream schools were more accepting or more supportive of children with disabilities.
An accepting culture could help mainstream schools address student bullying problems, she suggested.
"Mainstream schools would have to ensure that they had suitable specialist support on a regular basis for those students with disabilities."
Parents of disabled children should also be allowed to choose between sending their disabled child to a mainstream or special school, she said.
IHC advocacy director Trish Grant said school enrolment, access to the curriculum and being part of normal school life were difficult for many disabled children.
The complaints process could also be challenging for them and their families.
"They have difficulty getting any level of response or accountability when schools fail to deliver the law or education policy."
A report recommendation to make inclusive education an enforceable right was a step in the right direction, Ms Grant says.
Schools, boards of trustees and principals could then be held accountable for decisions which impinged on this right and the delivery of education to all students, she said.
To address bullying and harassment, the report recommended the Education Ministry implement a standard anti-bullying programme ensuring schools were safe for disabled students.
Negative attitudes towards disabled children were also addressed.
"What parents tell us is there is a real lack of accountability in some schools in the way they behave towards their child," Ms Grant said.
"Certainly disabled students experience really high rates of bullying.
"We think that is a violation of their rights in the learning environment."
Currently, IHC is seeking a declaration that the Education Ministry and schools are treating intellectually and physically impaired pupils unlawfully.
The Human Rights Commission agreed to take up IHC's complaint, originally filed four years ago, alleging state schools were discriminating against thousands of disabled pupils.
Ms Grant said a statement of reply had been filed by Education Ministry lawyers and discussions were currently underway regarding the IHC claim.
Should IHC succeed, the Government could be found in breach of the Human Rights Act and face orders for compensation.
The Education Ministry said issues raised in the Disability Convention report were not new.
Parents should work with the ministry to resolve any enrolment difficulties, special education group manager Brian Coffey said.
"Many schools are providing well for disabled learners but this annual report is a reminder that everyone in education should continue to work together to ensure every learner, including their family and whanau, are welcome at school and have every opportunity to participate."
Mr Coffey said a number of recommendations in the report were already being implemented, including anti-bullying programmes in schools.
