In a deposition taken on 9 September, Tom was questioned by Elizabeth McNamara, the lawyer for Bauer Publishing which he is suing for $50million over two 2012 stories that claimed he had "abandoned" seven-year-old Suri.
The 51-year-old acknowledged that he didn't see his daughter for more than 100 days, from 4 August, 2012, when they finished a week-long father-daughter trip to Disney World, until Thanksgiving that November.
Citing his intense filming schedule in London for his sci-fi thriller All You Need Is Kill, Tom said, "Unfortunately in this situation it was impossible."
He said that he phoned Suri nearly every day — although he admitted this was a poor substitute for seeing her in person.
"You have to work at it," he said of talking to a child on the phone. "I've gotten very good at it. I tell wonderful stories.
"I also find, you know, that Suri is a very happy child, and confident, and has a good sense of self."
His work commitments in London, and his concerns about media attention, also meant that Tom was unable to travel to New York for Suri's first day at school.
"If she had asked me to be there, I would have been there," he said. "I would have worked it out in any way I could."
He added that he was unable to leave the "gruelling" film shoot when Katie suggested he come to New York in October, and said there were other times when the former couple couldn't work out their schedules for a visit.
"Things change and there is different agreements, like in any divorce, where you work out schedules," he commented. "It's just a different set of circumstances. It certainly doesn't mean that I've abandoned my daughter."
In the wide-ranging, sometimes contentious, deposition, Tom was also questioned about the impact Scientology had on his split from Katie.
Revealing that Suri is no longer practicing the religion, Tom was asked whether his wife had left him to protect their daughter from Scientology. "I find that question offensive…," he responded. "There is no need to protect my daughter from my religion.
But when he was asked whether Katie had left him in part for that reason, Tom replied, "that was one of the many assertions, yes… There are many other aspects to the divorce."
The actor also acknowledged that his older children, Isabella and Connor, whose mum is Nicole Kidman, haven't had contact with Katie since the split in June 2012.