Scientologists used fear-based brainwashing techniques for Isabella and Connor, when they were aged eight and six repectively, reported Vanity Fair magazine.
"The central problem (in the marriage) was Nicole did not want to deal with Scientology," former high-ranking Scientologist Marty Rathbun said.
The actress, who is currently married to Keith Urban, is a Roman Catholic and she once stated she did not want their children raised as Scientologists.
Since the couple divorced, the church allegedly instructed Tom and Nicole's adopted children to reject their mother and her movies.
"They rejected Nicole - they've been instructed. They took a course, PTS/SP, Potential Trouble Source/Suppressive Person, for persons connected in their lives who are an SP," said John Brousseau, former Scientologist and bodyguard to church leader David Miscavige.
"Bella and Connor whispered to me, 'JB, Nicole is an SP! Our mom's an SP - we hate going and seeing her.' The Scientology world hated Nicole," he added.
The church also allegedly did not like Cruise's former girlfriend Penelope Cruz either. The Spanish beauty was dismissed as a "dilettante" after she refused to learn about Scientology.
