Some secondary principals say a lack of resources is forcing them to discriminate against children with special needs.
Their admission comes as lawyers finalise a Human Rights Review Tribunal case for the IHC alleging that schools are discriminating against such children.
The Secondary Principals Association surveyed its members because of the impending case.
Most of the 52 responding principals said they do not get enough funding for children with special needs and 21 said they indirectly discriminate against such children because of a lack of resources.
The association says that discrimination includes blocking children from attending school camps or using potentially dangerous equipment.
The IHC has welcomed principals' honesty and says the survey will strengthen the organisation's case.