The Thank You For Smoking actress reportedly infuriated Scientologist husband Tom Cruise with her insistence that three-year-old Suri attend the Catholic Charities Yawkey Centre For Early Education And Learning in Boston, Massachusetts.
A source close to the couple who are living in Boston while Tom shoots his latest movie Wichita - said: "Katie has been listening to her parents who are devout Catholics.
"She is not convinced by Scientology and has told Tom that she wants Suri to be educated as a Catholic as she was.
"They had been having huge problems agreeing on her school. To say they were having arguments it putting it mildly but Tom came around to the idea in the end."
Katie has reportedly not been seen at the Church of Scientology for more than five months.
Tom was raised Catholic but converted to the bizarre sci-fi cult in 1990.
