Morton - who also penned a biography on the late Princess Diana - claims: "Cruise is second in command. Across 90 nations, 5,000 people hear his words of Scientology."
Cruise and Miscavige are allegedly so close, Miscavige even joined Cruise on his 2006 honeymoon with third wife Katie Holmes.
Morton also alleges Cruise's split from second wife Nicole Kidman was caused by Scientology.
Fearing Catholic Kidman's influence on Cruise's life, leaders of the religion asked the 'Top Gun' star to take a course in 1999 pinpointing "those in his life who create difficulties".
In 2001, Cruise filed for divorce after almost 10 years of marriage.
In another outrageous claim, Morton speculates Cruise's 20-month-old daughter Suri with Holmes may have been fathered using frozen sperm from the religion's founder L. Ron Hubbard.
He alleges: "Some sect fanatics wondered if the actress had been impregnated with Hubbard's frozen sperm.
"Katie might have felt as if she were in a real-life version of horror movie 'Rosemary's Baby', in which a young woman is impregnated with the Devil's child."
Cruise has denied all claims in the book and is planning to file a lawsuit against Morton.
The actor's lawyer Bert Fields said: "It's a pack of lies. The book suggests Scientology somehow runs his career. I've represented him for over 20 years and I've never discussed his business with David Miscavige. It's poorly researched and badly written, and it's not really even about Tom Cruise, it's an attack on Scientology."
The Church of Scientology has also vehemently denied the claims.
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