The 'Mission: Impossible' actor is said to have enlisted the help of Church leader David Miscavige in the early 2000s to help him convince his then-girlfriend and 'Vanilla Sky' co-star to allegedly drop her Buddhist beliefs and convert to his religion.
Mark 'Marty' Rathbun, who used to be Inspector General of the Church, spoke out in a new documentary called 'Scientologists at War' on Britain's Channel 4, telling how top Scientologists were tasked with pandering to Tom's every need - including helping him recruit Penelope for auditing, which is the cleansing of negative influences in order to heighten spiritual awareness and access untapped potential.
Marty said: "Cruise started making some noises about getting some help [from the Church of Scientology, and] Miscavige had me drop me everything.
"I helped him on his divorce from Nicole and then I was auditing him and I was helping him get Penelope auditing. I was helping him in all aspects of his life."
The 50-year-old Hollywood superstar "became number one priority" for the Church, but Marty was left reeling when Miscavige - who was Tom's best man at his wedding to Katie Holmes - shunned him after all his efforts to help the A-list actor in the wake of his divorce from Nicole Kidman.
According to RadarOnline.com, Marty said: "Once Miscaviage was able to hobnob with Cruise again, he was done with me. He actually tried to denigrate me a little bit in Tom's eyes.
"I was his biggest opinion leader having salvaged his marriage, his kids, his family life - even his career. It was crazy. Miscavige had to try and undermine me in front of Cruise."
Tom and Penelope split in 2004 after three years together, with his Scientology beliefs later reported to be the main cause of their break-up.
Penelope is now married to Javier Bardem and the couple have a two-year-old son Leonardo and are expecting their second child.
Tom and Katie divorced in June 2012, after six years of marriage, and they have a seven-year-old daughter, Suri, together.