Rathburn told "Rock Center" he didn't approve what he claims the couple's kids were being subjected to during their sessions.
He explained, "He (Cruise) and I were intensively at it, auditing several hours a day over several months, so the kids were in the hands of Church of Scientology staff and they were being indoctrinated and they were reporting to Tom on how that was going in my presence.
"The initial indoctrination... was teaching them that certain people are anti-social personalities; they're suppressive people, and they started teaching them the characteristics of the anti-social personality... like their own mother."
Cruise's lawyer Bert Fields has refuted teh claims. He stated, "It is absolutely false that Mr. Cruise, or anyone else to his knowledge, did or said anything to lessen Connor or Bella's communication or relationship with their mother,"
A spokesman for the Church told Access Hollywood that the conversations between Cruise and Rathbun never happened, calling the former counselor an "ex-communicated self-promoter."
Scientolgy has been scrutinized in recent weeks after Katie Holmes filed for divorce from Cruise.