The National Secular Society has challenged the appointment of religious representatives to all Scottish local authority education committees.
In a letter to all newly elected councillors, the society suggests that committees should dispute a legal obligation to have three non-elected religious members.
The appointment of Church of Scotland and Catholic Church representatives to all Scottish mainland education committees, it argues, appears to conflict with the 2010 Equality Act, which obliges councils to act in a non-discriminatory manner in matters of religion and belief.
The society questions "why these two churches, alone of all denominations and religions, should have the privilege of nominating members of education committees. This is especially the case when the Catholic Church has the support of such a small proportion of the overall Scottish population".
It urges councillors to keep the positions vacant and to challenge the existing "discriminatory" arrangements, which "work against the principles of democratic representation on which the new councillors were returned".
Michael McGrath, director of the Scottish Catholic Education Service, said the involvement of church representatives on education committees recognised their long involvement in the establishment and provision of education, particularly in schools.
"While this may be an issue of annoyance to the National Secular Society, they should have the good grace to recognise the legitimate interest and the positive contributions of the churches in this area," he said.
"They should also accept that the churches represent a considerable force for good in society, involving a significant section of society in voluntary action and charitable fundraising."
No one from the Church of Scotland was available for comment.