The Scottish Secular Society said the Scottish Government should provide clear guidance on how religious theories about the origins of life are taught. The move comes after public concern over a recent incident in a Scottish school.
Children at a primary school in South Lanarkshire were given books donated by the Church of Christ. The books debunked evolution and advocated the Church of Christ's belief that earth is a few thousand years old. Illustrations showed humans and dinosaurs living alongside each other.
After protests from parents, the council launched an investigation. The headteacher and her deputy were moved to other duties in the education department.
The Scottish Secular Society said it had no problem with students understanding not everyone accepted the theory of evolution.
But it said the only place for creationism and intelligent design in Scottish schools was "within a discussion context in religious and moral education classes".
A Scottish Government spokesman said: "It is for a headteacher to decide, in full consultation with the local authority, what links a school should have with its local faith communities."