The Church of England has said the policy preventing them from showing an advert featuring the Lord's Prayer did not exist at the time they were trying to get the video into cinemas.
The advert received clearance from the British Board of Film Classification and the Cinema Advertising Authority, but the Digital Cinema Media (DCM) agency, which handles adverts for Odeon, Cineworld and Vue cinemas, has refused to show it.
Cineworld has multiplexes in Boldon and Middlesbrough, Vue has cinemas in Hartlepool and Gateshead, and Odeon has a branch at the MetroCentre.
The Archbishop of Canterbury has said it is "extraordinary" that Britain's biggest cinema chains have banned the advert.
The CoE has threatened legal action and said it is the victim of religious discrimination after they were told the minute-long video could cause offence.
The advert, produced by JustPray.uk, shows the Lord's Prayer being recited by a members of the public ranging from bodybuilders to children, and also features the Most Rev Justin Welby.
A CoE spokesman said it was initially believed that their minute-long advert had been approved and would be played before showings of Star Wars: The Force Awakens from December 18.
They were later informed that, due to a DCM policy not to run adverts which could potentially cause offence, the video would not be shown.
When asked for a copy of that policy, CoE was told there is no formal policy document but that it had been agreed with the DCM's members.
There is now a formal policy on the DCM's website, which states: "To be approved, an advertisement must ... not in the reasonable opinion of DCM constitute political or religious advertising."
As further clarification, it reads: "Religious advertising means: advertising which wholly or partially advertises any religion, faith or equivalent systems of belief (including any absence of belief) or any part of any religion, faith or such equivalent systems of belief."
The Archbishop of Canterbury told The Mail on Sunday: "I find it extraordinary that cinemas rule that it is inappropriate for an advert on prayer to be shown in the week before Christmas when we celebrate the birth of Jesus Christ.
"Billions of people across the world pray this prayer on a daily basis. I think they would be astonished and deeply saddened by this decision, especially in the light of the terrorist attack in Paris where many people have found comfort and solace in prayer.
"This advert is about as 'offensive' as a carol service on Christmas Day."
The Rev Arun Arora, director of communications for the Church of England, said the Church is "bewildered" by the decision.
"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," he said.
"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."
Stephen Slack, the Church's chief legal adviser, warned the banning of the advert could "give rise to the possibility of legal proceedings" under the Equality Act which bans commercial organisations from refusing services on religious grounds.
Terry Sanderson, the president of the National Secular Society, said: "The Church of England is arrogant to imagine it has an automatic right to foist its opinions upon a captive audience who have paid good money for a completely different experience.
"The Church does not hesitate to ban things that it deems inappropriate from its own church halls - things like yoga. The cinema chains are simply exercising the same right."
DCM were unavailable for comment.