State-run Community National Schools are to phase out the separation of children into different groups at certain times based on their religion.
The practice has been employed over the past decade to enable Catholic children to be prepared for the sacraments during the school day.
The Education and Training Boards, which run the schools, have confirmed that all new Community National Schools will no longer offer sacramental preparation during the school day to Catholic children, and that the practice will be phased out in existing schools.
When this new model of schooling was first designed a decade ago, Ireland’s Catholic bishops told the Department of Education that faith formation during the school day was a "minimum non-negotiable requirement" for their support for the new model.
A spokesperson for the country's Catholic bishops has said the decision by the state's Education and Training Boards to phase out the practice of separating children during religious instruction classes in Community National Schools "is soley a matter for Education and Training Boards Ireland and its members".
ETBI is the umbrella organisation representing what were formerly known as Vocational Education Committees (VEC's).
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Departmental documents received by RTÉ News show how school principals, teachers, parents, and educational authorities strongly objected to an initial decision to divide children into four different religious groups.
While the schools quickly moved away from this practice, most continued to separate non-Catholic children from Catholic classmates in order to facilitate sacramental preparation.
During the last academic year, however, many of the schools abandoned this practice too.
A recent Trinity College study found that children attending Community National Schools believed that Catholic pupils were being privileged over others because school time was being given over to allow them to prepare for the sacraments.
The study, carried out by sociologists at the university, also found that the State-run schools were having to negotiate with local Catholic priests on the amount of time they could dedicate to preparation for Communion and Confirmation.
The Head of umbrella body ETB Ireland told RTÉ news that Ireland’s 11 Community National Schools would continue to support pupils individual belief systems.
"Educate Together don't deal with the belief identity of a child," he said. "We do, and that is the difference between the two models."
However Educate Together said it supported and encouraged its pupils to learn about and develop appreciation and respect for people from all backgrounds.
The multi-denominational patron body said it had long argued and repeatedly advised successive Governments that the practice of faith formation within school hours in schools bound to treat children equally could not be legally justified.