IHC has lodged a complaint with the Human Rights Commission against the Government for what it says are "discriminatory" policies.
IHC claims disabled students are being prevented from participating fully at their local school.
IHC's advocacy director Trish Grant said while legislation and wider government policy supported a child's right to attend their local school, many students experienced significant difficulty accessing the support necessary to participate in school life alongside their peers.
"We know that many schools acknowledge their response to disabled students is limited by resourcing and other constraints. It is clear that government policy does not allow all schools to do their best by disabled students," she said.
"The Ministry of Education has indicated to us that schools and boards of trustees are ultimately responsible for the problems, not government, and that government will defend much of the complaint on this basis. Such an approach will not solve this problem."
Ms Grant said IHC had received affidavits from parents, schools, academics and professionals working in the education sector that supported the claim that government policy prevented disabled students accessing the curriculum at their local school.
"These policies and the accompanying practices are discriminatory," she said.
"One of the biggest problems schools face is the lack of resources. Many schools have no choice but to limit attendance whenever support is unavailable. Parents are often asked to contribute financially to teacher aide hours because of a funding shortfall, the only other option being that their son or daughter is sent home."
The aim of the complaint was to end the discrimination through remedies available under human rights legislation.
The Education Act stated that any child with special education needs could enrol and receive education at their local state school.
The Green Party said the situation was "a national disgrace" and it was backing the IHC's complaint.
"These problems have been with us for so long and have still not been addressed by the Government," education spokeswoman Metiria Turei said.
"Children and young people are not being given an adequate education, as guaranteed to them by New Zealand law."
Ms Turei said 44 per cent of Maori children were not getting eye or ear tests in primary schools, yet difficulties with sight and hearing were a leading cause of learning and behavioural problems in schools.