The Vatican interfered with the filming of Angels & Demons, according to director Ron Howard.
Howard told a news conference the Vatican used its influence "through back channels" to hamper filming of The Da Vinci Code sequel, starring Tom Hanks.
"When you come to film in Rome, the official statement to you is that the Vatican has no influence," he told reporters.
"Everything progressed very smoothly, but unofficially a couple of days before we were to start filming in several of our locations, it was explained to us that through back channels and so forth that the Vatican had exerted some influence."
Rome's diocese banned the team from filming in two churches as the film, which is based on a book by Dan Brown, did not conform to the church's views.
Special effects supervisor Ryan Cook told Italian film magazine Ciak: "The ban on filming put us in serious difficulty because we were not able to carry out the photographic surveys necessary to reconstruct the setting. So for weeks we sent a team of people who mixed with tourists and took thousands of photos and video footage."
But the Vatican has denied the allegations and a spokesperson said the comments were a publicity stunt.
The Da Vinci Code attracted criticism from the Catholic church as it suggested Jesus married Mary Magdalane and had a family that the church kept secret.
The new film once again features symbologist Robert Langdon, who must stop a secret society, the Illuminati, from destroying the Vatican. The film is set for release in the UK and US on May 19th.