Parents fear siblings will be split by a decision to limit enrolment numbers at multi- denominational schools.
The Department of Education is restricting enrolment at five Educate Together schools to a half-stream limit, which means just 13 new pupils will be enrolled next September.
The decision affects Educate Together schools in Castlebar, Tuam, Tramore, Trim and New Ross.
Parents and teachers at the five schools affected have begun a campaign to have the decision reversed.
The schools were informed they would be allowed a half-stream intake when they were granted permission to set up.
This was because they are situated in locations with low population growth, but have a demand for diversity.
Educate Together described the affected schools as "thriving" with growing waiting lists. It said the move would require them to turn away children and families.
It said the department's decision contradicts why the schools opened and flies in the face of Government claims that the Irish education system supports parental choice.
A statement from the Department of Education said Educate Together had been aware that the five schools would begin as half stream schools with an intake of 13 pupils.
It added: "This arrangement has been reflected in the department's engagement with the patron of the schools, Educate Together, and was reiterated in correspondence and communications with the schools concerned.
A case has been submitted by Educate Together to the Department of Education to further expand these schools and this is currently under consideration, according to the Dept statement.
Fianna Fáil TD for Mayo Lisa Chambers has called on the Education Minister to abolish the 13 pupil limit. The Department’s current position to limit enrolment to a half stream from September has led to an outcry from parents in Castlebar, she claims, who want to send their children to a multi-denominational school.
The deputy says the Department sanctioned the opening of the school, but now appears to be attempting to stifle its success by imposing enrolment restrictions. Demand for places in Educate Together schools is high and the Minister should be embracing their popularity and increasing places to give parents a range of educational options.
She raised this issue at a meeting of the Fianna Fáil front bench yesterday and says Fianna Fáil is now calling on Minister Bruton to ensure that these schools are given the resources to offer the full allocation of class places, and not be stymied by a flawed government policy.