One-time Scientology counsellor Marty Rathbun tells U.S. news show Rock Center he helped Cruise through his divorce from Kidman, but didn't approve of what he claims the couple's kids were being subjected to during their sessions.
Rathbun alleges Church of Scientology Celebrity Center staff in Los Angeles "nannied" and "tutored" Cruise's son Connor and daughter Bella when they were six and nine, respectively.
He says, "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 dismissed the claims, which featured in a preview on TV show Access Hollywood on Thursday (12Jul12).
He states, "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,"
And a spokesman for the Church itself tells Access Hollywood that the conversations between Cruise and Rathbun never happened, calling the former counsellor an "ex-communicated self-promoter".
Cruise and the Church of Scientology have become front-page news since the actor's third wife, Katie Holmes, filed for divorce at the end of June (12), amid reports his faith in Scientology was partly to blame.