Spokesperson for the Scottish Catholic Church, Peter Kearney, told Premier pupils could face exclusion from the religious life of the school in response to them being removed from religious assemblies.
He explained why the church held that position: "The school has to then respond to or react to that requests and if a parent says 'I don't want my child to attend a mass in school, or a carol service in school, or any form of religious observance' then it's reasonable for the school to assume that the parent doesn't want the child to be involved in any religious activities. So, the school has to take account of other things, such as a nativity play or for example an assembly where there might be hymns sung or fundraising for a religious-based charity.
"Parents would be advised that if they wish their child to have no part in the religious life of the school, that's what it means." He added that this wasn't common as most parents do not opt for this choice as they've chosen a religious education.
Secular and humanist groups in Scotland have said this is isolating non-religious children unfairly.
Gordon MacRae, Chief Executive of Humanist Society Scotland told Premier: "The proposal of the Catholic Church relates to the rights of senior pupils to opt out of Religious Observance (what is known as compulsory worship in England).
"Every state school in Scotland is a faith school - either nondenominational or denominational. Parents and pupils do not have the choice of a non-religious school. Parents already have the right to opt their child out of such activities in School."
He explained how he thinks this threat has come about because of Nicola Sturgeon's recent desire to adopt the UN's Convention on the Rights of the Child.
Among basic rights for children, Humanist Society Scotland say adopting this means that not allowing children to opt out of religious observance is not in keeping with the convention.
About this convention, MacRae said: "The Scottish Government's proposal to incorporate UN treaty on the rights of the child infers that they will follow England and Wales and allow senior pupils their own choice about religious observance. In response to this the Catholic Church is urging pupils and parents to be told that they will be isolated from other aspects of school life including fundraising, all school activities such as nativity plays.
"This is contrary to the Scottish Government's guidance on RO [Religious Observance] which states that pupils who are opted out should not be disadvantaged. Many Muslim pupils already opt their children out of RO in Catholic schools and there has been no suggestion of isolating them from the rest of the school community.
"This appears to be a calculated way to coerce senior pupils from upholding their personal freedom of religion and belief. I am confident that the Catholic Education Service are better informed than the bishops and will ignore this nasty bullying threat from their church leaders."
Responding to the argument that parents may be fine with one activity and uncomfortable with another, Peter Kearney from the Catholic Church replied: "There would really be a bit of incoherence for anyone who held that view. If they find participation in, let's say, a nativity play - which many would argue is an act or worship and probably does involve singing hymns - if they that not problematic...they may not have quite thought through their beliefs in any great detail."
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