The Church of England planned to run the spot before showings of Star Wars: The Force Awakens, which opens on 18 December. But the spot will not run on Odeon, Cineworld or Vue screens following the decision by DMC, which manages the advertising for those chains.
The ad is called "just pray" and opens on Justin Welby, the archbishop of Canterbury, walking through church grounds and beginning the Lord's Prayer in a voiceover. People from all walks of life in the UK then take up the prayer and each recite a verse.
The spot promotes the launch of the Church of England's justpray.uk website, which encourages prayer and offers tutorials.
A spokeswoman for DCM said: "Digital Cinema Media has a policy of not accepting ‘political or religious advertising’ content for use in its cinemas.
"Some advertisements – unintentionally or otherwise – could cause offence to those of differing political persuasions, as well as to those of differing faiths and indeed of no faith.
"In this regard, DCM treats all political or religious beliefs equally."
According to its website, DCM controls around 80 per cent of UK cinema advertising.
The Church of England's director of communications, the reverend Arun Arora, said in a statement: "The prospect of a multi-generational cultural event offered by the release of Star Wars: The Force Awakens on 18 December – a week before Christmas Day – was too good an opportunity to miss and we are bewildered by the decision of the cinemas.
"The Lord's Prayer is prayed by billions of people across the globe every day and in this country has been part of everyday life for centuries.
"Prayer permeates every aspect of our culture from pop songs and requiems to daily assemblies and national commemorations. For millions of people in the United Kingdom, prayer is a constant part of their lives whether as part thanksgiving and praise, or as a companion through their darkest hours.
"In one way the decision of the cinemas is just plain silly but the fact that they have insisted upon it makes it rather chilling in terms of limiting free speech. There is still time for the cinemas to change their mind and we would certainly welcome that.
"In the meantime people should visit the site, see the film themselves and make up their own minds as to whether they are upset or offended by it."