Remini, who was a member of the church until 2013, told The Daily Beast that Cruise received special treatment by Scientologists.
"Scientologists are told that Tom Cruise is saving the world single-handedly, so he is considered a deity within Scientology. He is second to David Miscavige— the savior of the free world. Tom is even called 'Mister Cruise' by staff members," she told the Beast.
The Kevin Can Wait star said that the church will go as far as to remove anti-Scientology materials from where they know he will be.
"They'll go as far as, if he's going to walk a certain place, they'll make sure there are no magazines that are anti-Scientology, so he can't see that," she said.
She posited that while many believe Cruise was "an innocent victim in all of this," like many other members of the church, he is actually allegedly "very aware" of what goes on inside the church.
"Where Tom is concerned, that is very different. He is very aware of the abuses that go on in Scientology. He's been part of it."
She told the publication that his close relationship with Miscavige is the root of his status in the church, calling him "not in the same category as the average Scientologist."
She said that an official inside the church told her Miscavige ordered Cruise to dole out punishment on a high-ranking member.
She also claims that one senior executive heard Miscavige use Cruise's name as he threatened to punish staff at Gold Base, the church's confidential international headquarters.
"David Miscavige constantly threatened the staff at Gold Base with bringing Tom Cruise to Gold Base and kicking their f—ing a—es," she said.
But the organization itself denies Remini's claims, saying she is using them to promote her Emmy-winning series Scientology and the Aftermath.
"The Church rejects all of Leah Remini's allegations as false," the church said in a statement provided to Fox News. "The interview is a PR stunt to promote her fake reality TV show. As long as the entertainment media will print Leah Remini's lies, her anti-religious bigotry will have a voice. Her brand of hate has dire consequences. Just last week, for example, the FBI released a report showing the alarming increase of hate crimes in the United States, including 1 in 5 traced to religious bigotry. Remini has gone out of her way to manufacture hate and instigate harm toward innocent people."
Remini has been outspoken against the church in recent years since leaving the organization after being an active member for 35 years.