The issue has been brought into the spotlight by a petition which has been lodged at the Scottish Parliament, supported by Secular Scotland – a lobby group campaigning for French-style separation of church and state – calling for a system in which parents would have to choose to "opt-in" if they want their children to participate in religious observance, for example in assemblies. Parents currently have the legal right to opt out and request that they do not want their child to do take part.
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Secular Scotland, however, has emphasised that it wants teaching in the classroom on religious issues to continue on courses such as religious education. However, a separate petition to Edinburgh City Council by secularists is calling for an end to all religious observance in the city's schools.
In response to the moves, the Catholic Church and Free Church of Scotland have now said that secularists should set up their own "non-faith" schools instead.
Michael McGrath, director of the Scottish Catholic Education Service, said religious observance was part of the "fabric of the community life" in Catholic schools and they would contest any effort to remove the statutory requirement for it. Some commentators believe that, after gay marriage, the issue of religious observation in schools may be the next battleground when it comes to "culture wars" in Scotland.
McGrath added: "Some secularist groups appear determined to dismantle any public signs of this country's religious traditions, values and practices. We would be happy for them to establish their own schools as 'non-faith schools', just as the Catholic community did in the 19th century.
"This would allow them to promote their own values, traditions and practices for those parents who wished to make that choice for their children."
Reverend David Robertson, minister of St Peter's Free Church in Dundee, called for a "root-and-branch" reform of the whole system.
"Let the secularists have their schools, teaching their values," he said. "And let the churches return to a system where we run state-funded Christian schools. This would give parents a real choice, and offer real diversity and equality in Scotland."
However, Caroline Lynch, chair of Secular Scotland, said she had concerns that entirely secular schools would lead to issues over segregation.
"There is a lot of religious intolerance in this country, a lot of suspicion between different faiths and between the faithful and non-believers," she said.
"We think that segregating children in schools adds to that problem, and wish to see children of all faiths schooled together to promote understanding of each others' views."
The Church of Scotland said it remained committed to "genuinely inclusive" religious observance being a fundamental part of the school curriculum. Reverend Sandy Fraser, convener of the church's education committee, added: "We would be against changing the present pluralist, comprehensive, non-denominational school system and, to that extent, we would be against secularist schools in the same way would not be asking for Church of Scotland schools."
The petition to the Scottish Parliament has collected more than 1100 signatures since it was launched a week ago. It is urging the Scottish Government to amend the Education (Scotland) Act 1980 by making religious observance an "opt-in" activity rather than an "opt-out" for all Scottish state schools, including faith schools.
Petition author Mark Gordon, from Greenock, said he found opting his five-year-old daughter out of religious observance had caused unexpected difficulties. "After a while we realised she was upset at being separated from her friends," he said. "We asked what she was doing and it transpired that she would sit in the school office for 20 minutes while the rest of the children were praying and singing hymns. The final straw came when she was taken to church by another teacher who was not aware of my wishes."
He added: "We want quite simply a flip of the law so the default position is opt-out and if you want religious observance, you opt-in to it.
"We do want religious observance removed completely but we don't feel that is a winnable case – what is a winnable case is adjusting it to suit everyone, and we think our petition does that."
But, just as organised religion is fraught with different factions, divides and schisms, not all secularists have backed the move. Some are committed to the ending of religious observance altogether.
Gary McLelland, chair of the Edinburgh Secular Society, said: "For us, religious observance has no place in the education system in 2013.
"If the petitioners did get this debated in the Education and Culture Committee or the full Parliament, as an organisation we would have no choice but to stand up for the complete removal of this.
"It would be absurd from my point of view to get a major debate on this legislation and for a secular campaign group to advocate for continuing religious observance."
Bob Barfoot, education officer at the Humanist Society Scotland and a former headmaster, said: "It is a useful first step, but our view is that religious observance should have no part in the state curriculum. Religion is a private matter, best left to families."
One of the central arguments to the case is the recent decline of organised religion in Scotland. Norman Bonney, emeritus professor at Edinburgh Napier University and a member of the Edinburgh Secular Society, said a recent Scottish Social Attitudes Survey found that less than half the population of Scotland have a religious faith.
"You have a clear disjunction between the beliefs and behaviour of the present day and the institutions, particularly with religious provision in schools, which is based on historical fact and not on contemporary requirement," he added.
The Humanist Society Scotland said it now has about 8000 members, compared to 300 in 2005. Secular Scotland, which was set up a year ago, said it has 532 members.
The petition to Edinburgh council, which is calling for the discontinuation of religious observance in non-denominational schools, was lodged by mother-of-one Veronica Wikman, backed by the Edinburgh Secular Society. It was debated by councillors last week and a report on the issue is now being prepared for consideration by the council's children and families committee later this year.
Wikman said she got involved in the issue when she found out her son was being taught that God created the world in six days and was word-perfect in "Creationist hymns".
But she said she did not choose to opt him out of religious observance as she believes parents are being faced with an impossible choice under the present system of religious observance.
Wikman said: "You don't want him put in a situation where he is going to be segregated from the rest of the class or even the rest of the school.
"You are put in this impossible situation in which you can choose between religious indoctrination or you can choose to have your child punished for your refusal not to have them indoctrinated."