A disability lobby group is suing the Education Ministry over alleged breaches of the Human Rights Act.
IHC says a lack of funding and other policies prompt schools to discriminate against children with special needs by discouraging their enrolments, refusing to take them all day, or excluding them from some activities.
IHC has been trying to take the case to court since it lodged a complaint with the Human Rights Commission in 2008.
In 2011 the commisson's Office of Human Rights Proceedings agreed to take the case to the Human Rights Review Tribunal but earlier this year said it would prosecute individual schools, not the ministry.
The IHC says that was not acceptable and it has decided to pay for the case itself.