Supporters of multi-denominational education are planning legal action against the Department of Education because they claim its policy on new schools favours the religious over them.
The move comes after two proposed multi-denominational schools in Navan, Co Meath, and Waterford city failed to secure temporary premises and consequently could not open.
Over 100 pupils who were planning to attend the schools will have to enrol in denominational schools in September.
However, a small number are expected to opt for home education.
Educate Together, which represents the multi-denominational sector, said the Department's policy that primary schools must first secure temporary premises before getting official recognition and a permanent site was "totally unacceptable".
Its chairman, Mr Paul Rowe, said the parents of the children in Waterford and Navan were being forced to enrol in denominational schools, which conflicted with their beliefs.
He said denominational schools found it easy to secure temporary premises and obtain recognition from the Department of Education.
They often had large land banks to do this, he said.
He said the Education Act 1998 required the State to provide parents with choice in education.
But the policy of requiring parents to source temporary accommodation contradicted this.
"It seems that unless you have property your most fundamental education rights can be denied," he said.
He said he favoured the Department providing sites and said the practice of parents depending on local football clubs and private interests for accommodation should end.
Educate Together and parents involved in the Navan and Waterford schools are seeking legal advice. Mr Rowe said it looked like the only route to get the policy changed.
He said the policy might also contravene equality legislation and this was being studied too. Lobbying politicians on the issue is also to begin.
According to Department of Education sources, the reason it requires parents and patrons to find temporary accommodation is that it would be highly costly for the Department to do so.
Educate Together, along with the Gaelscoileanna movement, has been challenging the dominance of primary education by the churches for the past few years.
It is now regularly consulted on major developments in primary education.
In a separate development, the group has reacted angrily to its exclusion from a plan on education provision in Portlaoise.
Mr Rowe claimed the plan did not include a survey of the local population on what kind of schools they would like to have.
He said the plan would govern education provision for the next 20 years.
This meant a multi-denominational school was unlikely in the area whose population is expected to reach 36,000 by 2020.