Professor Robert Davis has said there is evidence the views of high-profile atheist authors that religion is akin to "ghost-hunting or astrology" is now taking root in the education system.
The academic, who is head of Glasgow University's school of education and also professor of religious and cultural education, has called on teachers to ensure faith continues to be given its rightful place in the school curriculum.
A High Court ruling in London last week outlawed the centuries-old tradition of formal prayers being said at the start of local council meetings in England.
However, Mr Davis's comments were aimed primarily at the growing popularity of so-called new atheism – the name given to a movement which advocates the view that religion should not simply be tolerated, but should be "countered, criticised, and exposed by rational argument".
The new atheists argue recent scientific advancements prove the flawed nature of religious belief. And many of the books associated with the new atheism – including The God Delusion, by Richard Dawkins, and God Is Not Great: How Religion Poisons Everything, by Christopher Hitchens – have become worldwide best-sellers.
Mr Davis said: "The new atheism is campaigning and polemical and, through its high-profile spokesmen, it lobbies very powerfully for a particular version of the science curriculum, the study of biology, the understanding of human behaviour and human nature and the promotion of neuroscientific explanations of human emotional interaction.
"There is abundance of evidence the new atheism has very clear designs on the role of education in a democratic society and I think it has made a strong impact on schools and teachers and I think that has to be questioned."
Mr Davis said it was becoming "the norm" for teachers to see scientific study as the "standard method" by which to investigate all human phenomena.
"I am not suggesting the kind of questions the new atheists raise are not serious, legitimate questions that teachers should be aware of, but it does not seem to stop there," he said.
"They want to exclude other perspectives and suggest they are not only wrong, but are invalid and should not be given any kind of space in learning and teaching and that is where those attitudes become damaging.
"The Scottish curriculum is remarkably resilient and is deeply-rooted in consensus, but it is undoubtedly under pressure. Religion gets robbed of its right to be present in the curriculum and the new atheists would group serious religious enquiry alongside ghost hunting and astrology in terms of their intellectual validity – if you sell that perception successful to educators and the wider population you risk driving out all study of the major faiths."
Mr Davis said all schools needed to ensure they educated pupils in the ideas of their surrounding culture, including the debates about religion and religious belief and school.
"Violent, irrational, intolerant, allied to racism, tribalism and bigotry, invested in ignorance and hostile to free inquiry, contemptuous of women and coercive toward children: organised religion ought to have a great deal on its conscience."
"Faith is the great cop-out, the great excuse to evade the need to think and evaluate evidence. Faith is belief in spite of, even perhaps because of, the lack of evidence."
"It is time we admitted faith is nothing more than the licence religious people give one another to keep believing when reasons fail."