The actress filed for divorce from Cruise on Friday (June 29), allegedly over concerns that their six-year-old would be forced into adopting his beliefs.
Sources have now claimed that Holmes feared Suri would be put through a Scientology ritual called "sec checking", in which subjects hold electrodes so that their "areas of spiritual distress" can be identified.
The results are based on how the subject answers a number of deeply personal questions, including: "Have you ever decided you did not like some member of your family?", "Have you ever bullied a smaller child?" and "Have you ever gotten yourself dirty on purpose?".
According to TMZ, Holmes saw Cruise put Isabella and Connor, his children with ex-wife Nicole Kidman, through the process in 2005 and feared he would do the same to Suri.
It has already been widely reported that Holmes ended her marriage over threats that Suri would enter a military-esque Scientology compound called the Sea Organisation.
Members of Sea Org are apparently made to pledge their allegiance to Scientology for a billion years and are banned from leaving the base, which is said to have a sniper-style bunker.
According to the Daily Mail, members are paid just $50 (£31) a week, barred from having children, and are thrown into 'punishment trailers' known as 'The Hole' for bad behaviour.
Holmes is believed to be seeking sole custody of Suri, though Cruise reportedly wants to challenge this.
Photo gallery - Tom Cruise and Katie Holmes's relationship in pictures:
Copyright: Rex Features