The Church of Scientology has defended the use of NSW schoolchildren in an ad promoting the church, as the self-described "advanced organisation" goes on a marketing drive following the opening of its $37 million Asia-Pacific headquarters on Sydney's north shore.

The children, from Newtown's Athena School appeared in advertisement for the church alongside their principal Fiona Milne in July.

In the ad Mrs Milne said she "wasn't going to let children suffer how I'd suffered in the classroom", so she implemented the "clear" teaching techniques of L. Ron Hubbard in the classroom. Mrs Milne declined to comment on whether the school had obtained parental permission for the ad.

The church has strenuously maintained the school and the church are separate organisations. The school teaches the "Way to Happiness" philosophy of Scientology leader L. Ron Hubbard, but does not disclose that philosophy's link to the church on any promotional material.