The cult is being cited as the reason behind the meltdown of Cruise-Holmes marriage of five years.
Holmes was convinced that the 49-year-old actor would send Suri away to the Scientology organization known as Sea Organization, reported TMZ online.
Sea Org, as it is known, is where the highest levels of Scientology are taught and kids as young as five can be sent to live there without their parents and our sources say Tom is a big fan.
"Katie and Tom had been arguing over Suri's indoctrination into Scientology and the Sea Org was the flashpoint," a source close to Holmes told the website.
The Sea Org has been often compared to a boot camp and several ex-Scientologists (including Oscar winner Paul Haggis) have been outspoken against its military-like conditions.
Holmes herself has first-hand knowledge of the Sea Org. When she and Cruise first hooked up in 2005, Jessica Feshbach, a prominent Scientologist, who had been with the Sea Org since 1994, was transferred and became the actress' assistant.
"In the end Katie felt the only way to save Suri from being shipped off to Sea Org was to file for divorce and seek sole legal custody," the source added.