A senior figure in the Church of Scientology has been accused of trying to cover up the sexual assault of an 11-year-old girl in Sydney.

In an exclusive interview for ABC1's Lateline program, a former member of the Church of Scientology says she was coached by a senior figure in the church to lie to police about the abuse at the hands of her stepfather.

Carmen Rainer's mother Phoebe was a member of the Church of Scientology and went to the organisation for advice when she learnt her daughter was being sexually abused.

Police are now investigating claims Jan Eastgate, who was in charge of a church-founded organisation at the time, told both mother and daughter to lie to police and community services about the abuse.

Ms Rainer also says the church told her the abuse, at the hands of her then-stepfather Robert Kerr, was her own fault.

"They told me it was my fault because I'd been bad in a past life - I'd probably done something bad in a past life so I pulled it in," she said.

"I believed them. As a child I believed them. I was 11. That's what I knew. I grew up believing what they believed."

At the time, Ms Eastgate was head of the Citizen's Commission on Human Rights (CCHR) in Australia - an organisation founded by the Church of Scientology that campaigns against psychiatry.

She is now the international head of the CCHR, which is based in Los Angeles.

Ms Eastgate is accused of interfering with a police investigation by coaching Ms Rainer on what to tell police and community services.

Ms Rainer says Ms Eastgate told her to tell police she did not want her stepfather to go to jail and to tell community services he had not touched her genitals.

"'Just say no', she kept repeating that. 'You remember that you can't tell them.' Don't say yes because otherwise you will be taken away from your parents and you'll never see your family again because [Department of Community Services] will take me and my brother away from my mum and that I needed to just say no," she said.

Ms Rainer's mother also says Ms Eastgate told her to lie to police.

"Jan Eastgate coached both of us actually and she came with us to DoCS - they weren't called DoCS back then - but she came with us to the interview and she basically told me what to say and Carmen what to say and she also told Carmen to lie to the police and I lied to the police as well because of that," she said.

Ms Eastgate declined to talk to Lateline either on the phone or on camera.

In an email to Lateline she described the allegations by Carmen and Phoebe Rainer as "egregiously false".

"The family asked for my help to attend their meeting with Youth and Community Services specifically because they did not want anyone involved to be forced to undergo psychiatric treatment," she said.

"It had nothing to do with the merit of potential criminal charges."

Ms Eastgate and the Church of Scientology say Mr Kerr went to the police in 1999 at the church's insistence.

But Phoebe Rainer says Mr Kerr was told by senior scientologists he had to go to the police only after she threatened the church with legal action 13 years after the original allegations were made.

Ms Rainer says it was indoctrination that led her to agree to protect the Church of Scientology instead of her daughter - an act that has lead to a strained relationship.

"It would be hard for an outsider to understand why it would be done, but you are so totally brainwashed by their beliefs and then you get told that if you go this particular way you will lose everything, you will lose your future," she said.

Carmen Rainer has now made a statement to police outlining the allegations against Ms Eastgate and police are investigating the matter.

The Church of Scientology said in a statement the allegations were untrue and defamatory.