The central role of religion in the overwhelming majority of schools in the Republic of Ireland may be a breach of the human rights of some children.
And allowing pupils from minority faiths or none to opt out of religious instruction may not be enough to rectify the situation because the Catholic Church's ethos permeates the day-to-day life of most schools, a discussion paper has said.
The Government has been told it is time to address what place, if any, religion has in the classroom.
Ireland's record on religion in schools will come under scrutiny next year during a review by the United Nations Human Rights Council.
The Irish Human Rights Commission (IHCR) issued a discussion paper over the weekend, posing a number of questions as to whether the law and practice in Ireland fully meets human rights standards.
"To put it somewhat baldly, the core issue to be discussed concerns whether religion has a place in the classroom and, if so, what role should it play," IHCR president Maurice Manning said.
He said the Irish position faced challenges under the European Convention on Human Rights, International Covenant on Civil and Political Rights, the Convention on the Rights of the Child and the Convention on the Elimination of All Forms of Racial Discrimination.
The questions raised by the discussion paper included the rights of children in a rural setting who have no option but to attend a religious-ethos school.
At primary level, Catholic schools are required to devote two-and-a-half hours per week to religious instruction, while it is two hours per week at secondary level.
In the multi-denominational Educate Together schools, the issue of religious instruction is regarded as a matter for parents and, where it takes place, it is done outside of school hours.
Pupils may take Religious Education as a subject in Junior and Leaving Cert exams, but that involves a general study of world religions and beliefs and does not involve an assessment of a student's personal faith or commitment.
The IHCR paper notes that provision is made for the right of parents to withdraw their children from any instruction that conflicts with their own convictions.
However, because of the way that religion might informally permeate the school day in denominational schools, this right would not necessarily insulate such pupils from receiving religious education informally, it stated.
Dr Manning said the place of religion in the classroom was an issue with which all countries were grappling, but Ireland was somewhat unique internationally because religious orders had played a very prominent role in Irish education.
Ireland has a system of almost entirely denominational primary education, predominantly controlled by the Catholic Church, which runs about 92pc of primary schools. There are no non-denominational schools, and just over 2pc of schools are inter-denominational or multi-denominational.
While most people in Ireland define themselves as belonging to the Roman Catholic Church or Church of Ireland, a significant number now define themselves as being of no belief or of Islamic, Jewish, Buddhist, Hindu or other belief.
The paper was launched at a conference held in association with the School of Law at Trinity College Dublin, which kick-started a national consultation process.
Dr Manning said after the consultation process was complete, at the end of January, they would make recommendations to the Government on the measures required for the State to meet its human rights obligations in this area.