The school at the centre of Cruise split

Insiders claim Katie Holmes filed for divorce to prevent the Church of Scientology educating her daughter

Katie Holmes filed for divorce from Tom Cruise in an attempt to prevent her six-year-old daughter being educated at schools with links to the Church of Scientology, multiple sources claimed yesterday, adding to evidence that the controversial faith lies at the centre of the couple's split.

The blockbuster legal battle, which became public on Friday, has highlighted disagreements between Holmes and Cruise over their child Suri's relationship with the New Village Leadership Academy in Calabasas. The school educates children using "study technology", a technique created by Scientology's founder, L Ron Hubbard.

Holmes, 33, was raised a Catholic and is said to have concerns about Suri's religious upbringing. The Academy – which Suri was seen at in 2009, and again late last year – is officially secular, and employs "study technology" as just one of a range of educational methods. But several members of its teaching staff are Scientologists. The school is also considered a feeder to the Delphian School in Oregon, a $42,000-a-year boarding school which counts Tom Cruise and his ex-wife Nicole Kidman's adopted children Connor and Isabella, 17 and 19, among alumni. Up to half of its pupils are members of the church.

"[Suri] is coming to an age where she gets educated enough to get locked into the faith," Marty Rathbun, a former senior executive in Scientology told The Independent yesterday. "That's why there's almost certainly truth in the consideration that schools have started coming into play in all this."

Since news of the divorce broke, Holmes is said to have enrolled her daughter at a Catholic elementary school in Manhattan.

Cruise is Scientology's most celebrated member. He and Holmes were married in 2006, at a ceremony presided over by the church's leader, David Miscavige. But they are said to have had growing disagreements over how the faith should be applied to rearing their child.

"Scientologists believe in reincarnation, that infants are essentially ancient adults being in children's bodies," a source familiar with the dispute said. "Tom treats Suri as a little adult. Katie takes the opposite view: that she deserves a childhood."

Importantly, Suri has reached the age at which church members begin being "audited", a form of counselling at the centre of Scientology. A "security check" devised by Hubbard for use on six to 12-year-olds requires them to be asked personal questions while attached to an "e-meter", measuring electrical charges carried by their body. The list of questions includes: "have you ever gotten yourself dirty on purpose?" And: "have you ever told bad stories about someone?"

Holmes is apparently anxious to prevent her child from being subjected to any such "check". She is therefore reported to be seeking sole custody of Suri, a move that would give her the right to determine her religious upbringing and where she is educated. The actress filed for divorce in New York, while Cruise, 49, has counter-filed in Los Angeles. Both jurisdictions will take a similar view regarding the distribution of the couple's $275m fortune, but New York courts tend to grant sole custody, while joint custody arrangements are more common in California.

Holmes is perhaps also anxious to prevent history from repeating itself. When Cruise divorced Kidman, he secured a joint-custody agreement. The couple's children grew up as members of the church and today have a relatively distant relationship with their mother, who is not a Scientologist.

Mr Rathbun says he "audited" Cruise at Scientology's headquarters in Los Angeles between 2001 and 2003, when the actor was divorcing Kidman, and claims to have witnessed this process. He said he saw Connor and Isabella, who were six and eight-years-old at the time, being introduced to auditing.

"Everyone was thrilled to see Connor playing on an e-meter," he said.

The church did not respond to queries about that affair yesterday. But in the past, it has attacked Mr Rathbun's credibility, describing him as a "liar", a "criminal" and an "apostate".

Elsewhere, it was reported that Holmes was anxious to stave off an imminent effort to enrol Suri in the Sea Org, the church's clergy, which requires recruits to sign a billion-year contract.

But expert sources poured cold water on those particular claims, pointing out that the Sea Org does not typically welcome new members until their teenage years. Mr Rathbun said, however, that schools which employ "study technology" – an educational technique that revolves around rigid study programmes, repeated use of dictionaries and a strong emphasis on building clay models – can provide a long-term path to membership in the organisation.

"In the old days these schools would use study tech as a small part of a traditional curriculum," he said. "Now things have evolved, to the point where you hear of pupils are being assigned 'lower ethics conditions' and told to do auditing and getting an education which revolves around how to be 'good' Scientologists. Many of them are becoming a recruiting ground for the Sea Org."

The church has yet to comment on its role in the divorce, except to deny extravagant reports carried by the British tabloids that yesterday suggested that it had hired private investigators to follow Holmes around New York. Behind the scenes, a damage-limitation exercise is afoot. But it is hampered by the unfortunate absence of Jessica Davis, a church employee who has been its leading point of contact with Holmes for many years. The wife of Tommy Davis, Scientology's spokesman, she has been ill for some time. As a result, a church source said, "David Miscavige lost his lines of communication with Holmes some time ago".