Odeon, Cineworld and Vue cinemas are showing the short film, Sanjay's Super Team, which shows Hindu Gods acting as superheroes to protect a young boy.
In November, the same cinema chains refused to show an advert for the Lord's Prayer saying it could be offensive to people of other faiths and no faith at all.
The advert had been due to be shown before the new Star Wars film.
After initially agreeing the advert would be approved by Digital Cinema Media, it was then banned.
The Church said that every "advertisement conveys a message".
Revd Arun Arora, director of communications for the Archbishops' Council said: "I haven't seen the film but as someone who grew up watching Hindi films and brought up on Bollywood I have no problem whatsoever with Sanjay and certainly have no objection to the cinemas showing this film.
"But the fact that they are doing so demonstrates the incoherence of their on the hoof policy making.
"Every film and advertisement conveys a message.
"And this one seems to convey an obviously pro-religion, in this case pro-Hinduism one.
"There is an unfortunate combination of double standards and hypocrisy on display in this decision making process which needs addressing urgently.
"As Rowan Williams wrote recently, 'Advertising our Christian history is not intruding dangerous propaganda into a neutral and benign space. It is competing with existing propaganda, existing philosophies and ideologies.'
"All we ask is the opportunity to be heard. We remain hopeful that the cinemas will demonstrate the necessary strength of leadership, change their minds and show the justpray.uk film."
A spokesperson for Odean said that: "It is a film, not an advertisment, so it is not covered by our advertising policies."