The 33-year-old actress filed for divorce from the Hollywood star yesterday and is seeking sole custody of their child. The move appears to have taken 'deeply saddened' Tom, 49, by surprise, although the couple have not been seen together in public since February.
Katie, who was brought up as a Catholic, is said to be increasingly uncomfortable with Tom Cruise's views on bringing up children within the Scientology church.
Celeb blogger Perez Hilton reported an insider as saying: "Tom is nowhere near as strict as Katie is and doesn't believe in disciplining Suri, whereas Katie believes that's important. Tom basically treats Suri as a little adult, and that causes some major clashes over parenting style."
Katie recently started Scientology school wearing bright red lipstick.
Scientologists believe children are individuals, capable of making their own decisions.
In an interview in 2010 Tom echoed this approach when he said: "I say to Suri, 'I really want you to eat this protein if you're going to have that sugar.'
"She looks at me and she goes: 'Dad, I don't think you should try to force me to do something I don't want to do.'
"She likes to dress herself and wears whatever she wants. I'm not gonna tell her different."
Katie also reportedly filed for divorce in New York because it is not a no-fault state giving her greater chance of winning sole custody.
Shortly after the news was announced yesterday, TMZ claimed that as well as asking for 'primary residential custody' of Suri, Katie was asking for a 'suitable amount of child support'.
This figure is likely to be a staggeringly high one. Despite her age, Suri is already known for her extravagant wardrobe, including a designer shoe collection that's the envy of women three times her age.
Last year she came 21st in a list of Glamour magazine readers' style icons, beating Lady Gaga and Sarah Jessica Parker.
As her mother has looked increasingly careworn and preoccupied as she steps out of their New York apartment, straight into the glare of the paparazzi cameras, Suri has displayed a succession of glamorous outfits and even lipstick on her scowl. Even aged six, she frequently insists on being carried by her frail looking mother.
The popular spoof blog, titled Suri's Burn Book has been updated with the post: "Please respect my privacy during this difficult time. (Just mine though - everyone else is fair game.)
'"I will be vacationing in the Cayman Islands for the Independence Day holiday with my financier, and going over my plans to seek sole custody of myself.
"I appreciate the concern and the warm wishes."
The divorce looks set to become bitter, with both parents feuding over control of Suri. Let's hope this little girl is not too affected by a divorce played out in public and gets the chance to enjoy the semblance of a normal childhood.