The Top Gun star is suing bosses of In Touch and Life & Style magazines over reports alleging he "abandoned" the couple's daughter Suri following their split last year (12).
At the time of their divorce, rumours suggested that his close involvement with the Church of Scientology was a factor in the break-up, and now it has emerged Cruise admitted Holmes cited the religion as one of her reasons for wanting to end the marriage.
Documents from the case show that during a court questioning in September (13), Cruise was pressed to confirm or deny the rumours by lawyers representing the magazines.
Asked if Holmes had "indicated" that one reason for their split was "to protect Suri from Scientology", he replied, "Did she say that? That was one of the assertions, yes."
However, according to New York Post gossip column Page Six, Cruise later asked to change his statement, insisting, "Katie has never told me that this was a reason for our divorce."
During the hearing, Cruise also defended himself against allegations he did not see Suri, now seven, for more than 100 days after splitting from Holmes, saying, "When a divorce occurs, things change... now you have to ask for permission and organise schedules to make things happen... It's not an ideal situation... Things change. And certainly what doesn't change is the love that I have for my daughter, the fact that I didn't abandon her emotionally, physically or otherwise."
The defamation case is due to begin at a court in New York City next week (beg11Nov13).
Cruise and former Dawson's Creek star Holmes split last year (12) after five years of marriage.