Dr Rowan Williams, the Archbishop of Canterbury, used his traditional Christmas Day sermon at Canterbury Cathedral to launch the broadside.
He said President Jacques Chirac's support for a law banning religious symbols such as the Islamic hijab was unsurprising "in a secular environment that looks at religion not only with suspicion or incomprehension but with fear".
"The proposal to ban Muslim headscarves in French schools suggests that there is still a nervousness about letting commitment show its face in public," he said.
"Discomfort about religion or about a particular religion may be the response of an educated liberal or, at the opposite extreme, the unthinking violence of an anti-Semite.
"It isn't easy to face the fact that sometimes the effects are similar for the believer."
The Archbishop, who represents 70 million Anglicans worldwide, also spoke out against religious extremism and intolerance.
"Alas," he said, "religious faith has too often been the language of the powerful, the excuse for oppression, the alibi for atrocity."
"Discomfort about religion or about a particular religion may be the response of an educated liberal or, at the opposite extreme, the unthinking violence of an anti-Semite. It isn't easy to face the fact that sometimes the effects are similar for the believer"
Dr Rowan Williams,
Archbishop of Canterbury
And he said religious intolerance was being given a new lease of life "by the threat of terror carried out in the name of a religion - even when representatives of that religion at every level roundly condemn such action as incompatible with faith".
Dr Williams has been preoccupied with relations between Christians and Muslims over the past year and was a leading critic of the US-led war on Iraq.
He has also criticised the holding of Muslim prisoners without trial by the United States and Britain, saying this complicates relations with followers of Islam.
President Chirac last week declared his support for a ban on "conspicuous" religious insignia after an advisory committee said they contravened French schools' secular nature.
He indicated he would like to see the ban written into law by the start of the next academic year.