Mike Rinder's new book, "A Billion Years: My Escape From a Life in the Highest Ranks of Scientology," is peeling back the layers of the always-secretive world of Scientology ... and Mike's revealing a time when the Church began to drive a wedge between Tom and Nicole.

Mike claims the church got worried when Tom began ignoring calls from Church honcho David Miscavige ... while away filming Kubrick's "Eyes Wide Shut" in London.

Miscavige was super worried he might lose his grip on Tom, so he sent a top exec to the UK to audit the actor -- meaning he'd be walked through the negativity in his life to become "clear" once again.

Mike claims Tom eventually returned to the fold, which caused a serious divide between him and Nicole. He says the Church was so threatened by Nicole's influence, they allegedly hired a PI to spy on her and tap her phone.

The Church denies the wiretapping claims ... telling Page Six, "Mike Rinder is an inveterate liar who seeks to profit from his dishonesty. He supports himself by orchestrating the harassment of his former Church and its leader through false police reports, incendiary propaganda and fraudulent media stories.”