The Principals' Federation says schools have a hard time incorporating some children with special needs into classrooms because of their behaviour or communication skills.
The IHC is taking a case against the Ministry of Education to the Human Rights Review Tribunal, claiming its systems and policies have led to discrimination against disabled children.
Federation president Phillip Harding says no one would condone a parent being told at their first interview that their child will not be allowed to enrol.
Mr Harding says there is not enough money to fund special needs students and there is evidence that teacher aides may discourage pupils from becoming independent.
