Education Minister Ann Tolley is threatening to take over the setting of integrated school fees if she finds schools are placing unreasonable demands on parents.
Integrated schools can charge fees, but only to cover property costs.
Mrs Tolley says she has had reports that some integrated schools are demanding large so-called voluntary fees from parents on top of "compulsory donations".
The minister has warned schools they may not set their fees higher than is justified by property expenses, or in order to fund facilities to a higher quality than other state schools.
Private schools that have become part of the state school system can still charge fees to cover property costs.
An association representing state integrated schools admits some are asking parents for significant amounts of voluntary payments.
The Association for the Proprietors of Integrated Schools says as a result of Mrs Tolley's comments, it will be working with schools to ensure that the minister gets what she wants.
Mrs Tolley's hard line with the sector comes as integrated schools are seeking up to $80 million for what has been described as urgent repairs.
The minister says demanding extra funding is not acceptable. She says she does not want to set maximum rates, but that is where the matter is heading if the issue cannot be resolved.