Parents of pre-school children are being surveyed by the Department of Education about what religious ethos they want the schools in their area to have.
It is part of the latest move to reduce the influence of the Catholic Church over education.
The result of the surveys with parents will feed into discussions with Catholic bishops about handing over patronage of some schools to meet any demand for change.
At the moment 90% of primary schools are Catholic controlled.
Educate Together has called for the surveys to be independent.
"Educate Together has called for the initial surveys of pre-school children to be strictly independent of any existing school patron and that the surveys should immediately ask parents what ethos of school they want for their children," said Paul Rowe, CEO.
"This then should be used by the Department to allocate the patronage of any school identified for change. This programme needs dedicated funding in the coming Budget."