The "Mission Impossible" actor classified the claims as "patently false" and wrote that that in the months following the divorce he and Suri "spoke on the phone nearly every day" in court papers filed Tuesday in his ongoing $50 million lawsuit against Bauer Publishing Co., the publisher of In Touch and Life & Style magazines.
Photos: Tom and Katie Before Split
"She is a very happy child and we have a wonderful relationship and cheerful phone calls," Cruise, 51, wrote of his now 7-year-old daughter. "She has never indicated, in words or substance, that she has ever felt abandoned by me."
Cruise's two-page description of his relationship with his youngest child, his only child with Holmes, is part of a lawsuit he first filed in October of last year stemming from a pair of 2012 cover stories in Life & Style and In Touch.
According to the lawsuit 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.
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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."
The stories inside the headlines claimed that Cruise was overseas shooting films immediately after his divorce from Holmes, leaving Suri in her care.
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."
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."
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.
"He understands that this kind of criticism goes with the territory with being one of the biggest movie stars in the world, but this one struck him wrong," said Hollywood publicist Howard Bragman, vice chairman of Reputation.com.
Cruise's lawyer, Bert Fields, told gossip website TMZ that the actor plans to donate any money he possibly gets from the lawsuit to charity.
ABC News reached out to both Cruise and Brauer Publishing, but neither responded.