The two churches are architectural jewels in the heart of Rome
The diocese of Rome has banned filming in its churches of the prequel to the Da Vinci Code, a popular book and film that has angered many Catholics.
Producers of Angels and Demons were turned down because the film "does not conform to our views", a spokesman for diocese told AP news agency.
The Da Vinci Code in 2006 was based on the idea that Jesus Christ married Mary Magdalene and had children.
It also depicted a conservative Catholic movement as a murderous cult.
The diocese of Rome said it had barred the producers from filming in its two famous churches of Santa Maria del Popolo and Santa Maria della Vittoria in the heart of the Italian capital.
"It's a film that treats religious issues in a way that contrasts with common religious sentiment," Monsignor Marco Fibbi, the diocese spokesman, told AP.
"We would be helping them create a work that might well be beautiful but that does not conform to our view," he added.
Angels and Demons, directed by Ron Howard and starring Tom Hanks, is expected to be released next year.