The mother-of-four, 51, spoke of her adopted children Isabella, 25, and Connor Cruise, 23, having “made choices to be Scientologists”, but she respected their decision.
She told Australia’s Who magazine : “They are adults. They are able to make their own decisions. They have made choices to be Scientologists and as a mother, it’s my job to love them.
“And I am an example of that tolerance and that’s what I believe – that no matter what your child does, the child has love and the child has to know there is available love and I’m open here.”
The actress’s reference to her children’s religion has refuelled speculation of why her 10 year marriage to Tom broke down in February 2001.
Although she made no secret of her heartbreak at the time, in hindsight Nicole admitted being married to such a high-profile Hollywood star, now 56, had “cocooned” her from reality.
Now happily married to country singer Keith Urban , Nicole said she felt “like I had to grow up” following the end of her relationship with Tom.
Tom and Nicole married on Christmas Eve 1990 following a whirlwind relationship that began on the set of Days Of Thunder the previous year, when the actor was still married to actress Mimi Rogers.
During their marriage, Nicole’s career took second place to Tom, who was one of the most in-demand actors in Hollywood.
They ended up adopting Isabella and Connor together after struggling to conceive naturally.
Eighteen months before their marriage, they filmed racy thriller Eyes Wide Shut, which many speculated had contributed to the breakdown of their relationship.
However, Nicole said in 2012: “People thought that making the film was the beginning of the end of my marriage. But I don’t really think it was. Tom and I were close then.”
Although Tom was a committed Scientologist during their marriage, it appears Nicole – who was raised Catholic – never became one.
In an interview following their divorce, Nicole admits she looked into it: “Tom is a Scientologist. I’m not. I was introduced to it by him, and I explored it. But I’m not a Scientologist.”
Threes years before their shock split, Nicole publicly distanced herself from the controversial religion, when she said: “I wouldn’t classify myself as a Scientologist, but my husband is.”
The Oscar winner’s public dismissal of the religion apparently didn’t go down well at the Scientology headquarters.
Tom shocked Nicole when he suddenly ended their marriage without warning on 4 February 2001 and announced their separation publicly the following day.
Divorce papers at the time said Nicole “protested [Cruise’s] intention to dissolve their marriage and urged him not to leave but to enter marriage counselling with her, or take other steps to address whatever problems may have existed in their marriage… Tom said his decision was final and he departed the parties’ home.”
The Church of Scientology and Tom have always denied the religion had anything to do with his marriage breakdown with Nicole.
Speaking about their coupling years later, Nicole said: “I would work, but I was still very much cocooned. So when I came out of it at 32, 33, it’s almost like I had to grow up.”
After their divorce was finalised, it appeared Isabella and Connor chose to live with their father and have been rarely seen with Nicole in recent years.
Isabella and Connor were last pictured with their mother in 2006 – the year she married Keith in a Catholic church ceremony in Sydney.
Both Nicole and Tom weren’t in attendance at Isabella’s wedding to Max Parker in 2015, while her daughter was not at her grandfather Antony Kidman’s funeral in 2014.