A petition to remove Church representatives from local authority education committees has been submitted by secularists to the Scottish Parliament in Holyrood.
The petition, submitted by Mr Colin Emerson on behalf of Edinburgh Secular Society, has received over 1,700 signatures.
The current law requiring three external religious nominees to be appointed to every Scottish local authority education committee should be rescinded, the group says.
The Edinburgh Secular Society (ESS) said: "To afford a particular section of society a privileged position within the decision making process of local government, based solely on their particular and personal religious beliefs, is profoundly and inherently undemocratic, unfair and discriminatory. It strikes against those specific virtues of justice and integrity underpinning our society and which lie at the heart of the Scottish Parliament."
It said the current set-up was outdated and entrenching sectarianism by requiring the appointment of at least one Roman Catholic and one Protestant nominee.
The group also suggested minority faith and non-religious groups likes humanists and spiritualists were being discriminated against because of the legal requirement that religious representatives have a "recognised place of worship".
With the 2011 Social Attitudes Survey showing that around 65 per cent of young people aged 18 to 25 have no religious affiliation, the ESS suggested the Church should not be on the committee because it is not truly representative.
The group also dismissed the Church's claims to act with impartiality, citing documentation from the Church of Scotland's General Assembly estimating that Church representatives "hold the balance of power" on 19 Local Authority Committees.
The coalition of groups behind the petition includes the National Secular Society, Humanist Society Scotland and University of Edinburgh Humanist Society.
Patrick Harvie, MSP for Glasgow, is quoted in the petition's background materials as saying: "In a society in which increasing numbers of people don't practice any religion, it's high time that we questioned a practice which gives religious hierarchies an influence over every child's education.
"I'm particularly concerned at the involvement of people who would promote utterly unscientific notions like creationism; pushing this absurd ideology at children is the very opposite of education."
Sandy Howat, City of Edinburgh Councillor said on the petition's website: "Unelected, unaccountable and I would suggest untenable? Undemocratic influence over public education is fundamentally at odds with the principles of respect, equality and shared freedoms.
"All contributions to committee deliberations should be welcomed, yet continued undemocratic privilege of the few over the many is an outdated tradition we should remove.
"As we look to create a fairer Scotland with liberty at its core, we need to ask ourselves what this 'privilege' says about our values; it's time for a new enlightenment."
Bailie Dr Nina Baker, Glasgow City Councillor said: "Whilst I can see that representatives of major world faiths might have a role in advising on curriculum content for the teaching of comparative religion in schools, I believe they should have no right to vote on councils' decision-making bodies.
"Those votes should be reserved for accountable, elected members only. A recent contribution from the Roman Catholic representative on Glasgow's executive was to make clear his Church could never accept the principle and practice of shared-campus schools, a policy with full cross-party support."
The Reverend David Robertson, Free Church of Scotland minister in Dundee and director of the Solas Centre for Public Christianity, challenged the petition and its aim.
He said in a statement: "It's sad that MSPs are having their time wasted by the continuing campaign of militant atheists seeking to impose their own philosophy on every child in Scotland."
Highlighting the fact that it was the Church of Scotland that founded the Scottish education system, Mr Robertson said: "If the Edinburgh Secular Society is serious about equality and diversity in our pluralist society, then they should be encouraging Christian schools rather than campaigning to remove the last vestiges of our once proud Scottish Christian education system."
A Free Church of Scotland spokesman added: "From today's questioning at Holyrood is it clear that the Edinburgh Secular Society does not really want more democracy, choice and freedom in Scottish schools, but simply they wish to ban anyone who does not agree with their world view from taking part in education."
A Church of Scotland spokesman was quoted in The Scotsman as saying: "The role representatives play is one of service and support that reflects its contribution to education since its vision of a school in every parish helped in establishing Scotland's universal education system, one of the first anywhere in the world, and profoundly shaped the Scotland we know today."
A Catholic spokesman, also speaking in the Scotsman, said: "Church representatives offer an invaluable service to their local communities by contributing to discussions among elected representatives on councils."