The Department of Education has reversed a decision to require State-run post-primary schools to provide an alternative subject choice to students who do not wish to study religion.
It has issued a circular, to replace one issued last February, which withdraws the alternative subject requirement.
Last February schools run by State Education and Training Boards, as well as community schools, were told of the new rules that would apply from this September.
However, the new instructions were ignored by schools and Freedom of Information documents received this week by RTÉ News show that the Catholic Church, as well as the ETB sector, objected strongly to the new alternative subject choice requirement, and lobbied for their withdrawal.
In a new circular issued today, the Department of Education draws a distinction between "religious instruction/faith formation" and religious "education".
It says that parents must "opt in" their children to any denominational religious instruction that the schools are offering.
However, it states that schools may follow the Religions Education programme drawn up by the National Council for Curriculum and Assessment, which it says is not delivered from any religious perspective.
It also states that classes following the NCCA syllabuses "cannot have any element of religious instruction or worship".
However, the circular issued to schools last February stated that "the NCCA curriculum also serves to meet the religious instruction requirements of the Catholic Church".
It said that schools should make parents fully aware that the curriculum "is not necessarily confined to learning about religions".
In a statement accompanying the publication of today's circular, Minister for Education Richard Bruton said it was "a clarification".
He said it was important that State-run schools operated as multi denominational schools and that the NCCA Religious Education curriculum, "is not taught with any element of religious instruction or worship".
Meanwhile, Atheist Ireland has said it is very concerned that the new circular could be a "nod and wink" exercise which may result in ETB schools, and the teacher unions, maintaining current practices under a different name.
It said it would be even worse if the new circular meant students were now not allowed to opt out of religion, contrary to their constitutional rights.
The organisation said February's instruction gave students the right to an alternative timetabled subject and it wanted to ensure that this happened.
It added that the NCCA syllabus does not meet the human rights test of respecting the philosophical convictions of parents and students.