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Tom Cruise hasn’t seen his daughter Suri, 10, in nearly three years because the Church of Scientology forbids its members from associating with nonbelievers, sources say.

Since his ex-wife Katie Holmes is not a Scientologist, and neither is Suri, Cruise has reportedly not seen his daughter since she was 7.

“If he wanted to see her, he could see her,” one source said. “Even people in prison have a right to see their children.”

Holmes spokeswoman Leslie Sloane had no comment, and Cruise’s publicists didn’t get back to me.

Suri, who lives and goes to school in Manhattan, is said to be a smart, well-behaved girl.

“She’s thriving. She’s got lots of friends and a nice, normal life. This is his loss, his issue, his problem,” said my source. “He must be really brainwashed.”

In Touch first reported it’s been 1,000 days since Cruise saw his daughter, even though Cruise sued the magazine’s parent company, Bauer Publishing, in 2012 for reporting that Cruise had “abandoned” Suri.

The $50 million defamation suit was settled the following year on undisclosed terms, with each side paying its own legal fees.

Tony Ortega, who writes about Scientology on his website TheUndergroundBunker.com, told me Holmes qualifies as an SP, suppressive person, in the cult-like group, and Suri would be deemed a PTS, potential trouble source.

“But the thing about Scientology is, celebrities get to break all the rules,” says Ortega. “That’s why I find this so mysterious.”