The Archbishop of Wales, Dr Barry Morgan, has described a rise in "fundamentalism" as one of the great problems facing the world.
Dr Morgan said fundamentalism left 'no room for debate'
He focused on what he described as "atheistic fundamentalism".
He said it led to situations such as councils calling Christmas "Winterval", schools refusing to put on nativity plays and crosses removed from chapels.
The National Secular Society has said Christians in the UK have "nothing to complain about".
In his Christmas message, the archbishop said: "Any kind of fundamentalism, be it Biblical, atheistic or Islamic, is dangerous."
The archbishop said "atheistic fundamentalism" was a new phenomenon.
He said it advocated that religion in general and Christianity in particular have no substance, and that some view the faith as "superstitious nonsense".
As well as leading to Christmas being called "Winterval," the archbishop said "virulent, almost irrational" attacks on Christianity led to hospitals removing all Christian symbols from their chapels, and schools refusing to allow children to send Christmas cards with a Christian message.
He also said it led to things like "airlines refusing staff the freedom to wear a cross round their necks" - a reference to the row in which British Airways (BA) suspended an employee who insisted on wearing a cross necklace.
Dr Morgan said: "All of this is what I would call the new "fundamentalism" of our age. It allows no room for disagreement, for doubt, for debate, for discussion.
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"It leads to the language of expulsion and exclusivity, of extremism and polarisation, and the claim that, because God is on our side, he is not on yours."
He said the nativity story in St Luke's Gospel, in contrast, had a "message of joy and good news for everyone".
He said: "God is not exclusive, he is on the side of the whole of humanity with all its variety."
Dr Morgan said it was "perfectly natural" to have a "coherent and rational debate about the tenets of Christianity".
But he said "virulent, almost irrational" attacks on it were "dangerous" because they refused to allow any contrary viewpoint and also affected the public perception of religion.
This month community cohesion minister Parmjit Dhanda said the UK should "celebrate" the role of Christianity in the country's heritage and culture.
His comments came after Mark Pritchard, Conservative MP for The Wrekin, called a Westminster debate on "Christianophobia", saying attempts to move Christian traditions to the "margins" of British life had "gone far enough".