Faith-based classes can still be held outside school hours
Communions and confirmations are off the timetable for State-run primary schools.
Instead Community National Schools will leave faith formation to parents and parishes.
Equate, which lobbies for equality in education, has welcomed the move saying religious discrimination has no place in schools.
While the schools are multi-denominational, some had allowed for communion and confirmation classes during school hours.
That is now being phased out.
Seamus Conboy works with Education and Training Boards Ireland - who run the 12 community national schools in greater Dublin and Cork.
He says parents can still arrange faith formation classes outside of school hours.
"We realised that we had to treat all children equally in relation to how we provide for their faith, so that was why we moved towards moving the sacramental education of outside the school day.
"Our school day is dedicated to the holistic development of the child in terms of their intellectual and moral development.
"Any group can use the school after school for specific faith formation".
The move has been welcomed by Equate, whose director is Michael Barron.
He is hopeful it will start a conversation in other schools.
"We think it's really important that no child is disadvantaged because of their religion or their beliefs, and rescheduling sacramental education outside of school time goes a long way towards doing this.
"It's very important that in our State-funded school system no child is disadvantaged because of their religion, and no religion has preference over another".