The new regulation, which comes into effect immediately, will affect pupils who previously were required to remain physically in the classroom even if they did not want to be there.
A statement sent to state schools by the Department of Education acknowledged that the past practice of assuming pupils are predominantly Catholic and arranging the teaching of religious studies accordingly was inappropriate.
Minister for Education Richard Bruton said: "It is important that Education and Training Board (ETB) and Community Post Primary schools, as multi-denominational schools, fully implement this circular as it presents an important opportunity to meet the expectations of parents and students in a changing society.
"This can only be achieved by consulting with parents, and including their wishes as part of the normal planning process of any school."
The new rules means parents and guardians will no longer be required to request a withdrawal from the subject for their child and children will be allowed to opt out of religious ceremonies such as masses held during school time.
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