Nov. 9, 2013— -- During a deposition in his court battle against a pair of magazines, Tom Cruise admitted that ex-wife Katie Holmes filed for divorce "to protect Suri from Scientology," according to court documents.
The "Mission Impossible" actor is embroiled in a $50 million suit against Bauer Publishing Company, the publisher of In Touch and Life & Style magazines over claims that he "abandoned" his daughter Suri after his June 2012 divorce from Holmes.
Cruise is asked by one of Bauer's attorneys whether one of the reasons that Holmes left him was "to protect Suri from Scientology," according to the transcript of Cruise's Sept. 9 videotaped deposition obtained by ABC News.
"Did she say that? That was one of the assertions, yes," Cruise said.
Holmes, 34, filed for divorce from Cruise in June 2012 after nearly six years of marriage. The pair "amicably settled" their divorce less than two weeks later but did not release details of the settlement.
At the time of the divorce, the former couple released a joint statement saying they were, "committed to working together as parents to accomplishing what is in our daughter Suri's best interests."
Cruise said Holmes was a practitioner of Scientology before and during their marriage, but left the church once she divorced him in June 2012, the court documents said.
While he did not pursue legal action against publications that claimed Holmes left him "in part to protect Suri from Scientology," he sued Bauer over the stories they ran concerning Cruise's supposed abandonment of his 7-year-old daughter, which he called "disturbing," according to the deposition.
"'He chose Scientology over Suri for good.' 'Has he chosen Scientology over Suri for good?' 'Abandoned by Daddy.' I mean come on, that is absolutely disgusting," Cruise said. "I tolerate a tremendous amount and I'm very privileged to be able to have the life that I have, and I believe that. But there is a line that I draw for myself and -- and that's it. And I asked for an apology. I asked for a retraction. They denied it."
While Cruise would not answer whether Suri practiced Scientology since his divorce from Holmes, he said his daughter was not currently practicing the religion, according to the court documents.
According to the suit obtained by ABCNews.com, Cruise's lawyer sent the publishers of Life & Style a letter on July 18, 2012, objecting to its July 30 cover headline "Suri in Tears, Abandoned by Her Dad" and story entitled "Suri's Emotional Struggle." In the letter, the lawyer said that the actor had spoken to Suri regularly while he was shooting a film and had been with her the day before the issue was published.
A story headlined "Suri's Emotional Struggle" was printed in Life & Style's July 30 issue.
In addition to the July report, the lawsuit references an Oct. 1, 2012, issue of In Touch, the cover of which showed a photograph of Suri with the headline "Abandoned By Daddy."
Cruise said that he saw his daughter a total number of 10 days between June and Thanksgiving of 2012.
Cruise writes in his court filings that he was working overseas on two films at the time, but says that he never cut Suri out of his life, "whether physically, emotionally, financially or otherwise."
Suri now lives primarily in New York City with Holmes, who has been in South Africa filming "The Giver," with Taylor Swift. Holmes brought her daughter with her to South Africa and the pair were spotted together in Cape Town last month, according to a report in Us Weekly magazine.
Bauer Publishing filed court documents of its own in the case, writing that, at the time of publishing, Cruise had not seen his daughter in 44 days. The company claims Cruise was out at clubs and bars and vacationing, when he could have been with his daughter.
If Cruise prevails in his lawsuit, it would mark the first time the actor has successfully sued tabloids for stories involving his children, who, in addition to Suri, include a son and daughter with actress Nicole Kidman.
ABC News reached out to representatives for both Cruise and Holmes, but neither immediately responded.
Cruise's attorneys did not immediately respond to ABC News' requests for comment, and neither did representatives from the Church of Scientology.