Schools associated with the Church of Scientology are receiving more government funding per student than hundreds of Australian public schools, new data has revealed, despite benefiting from generous private donations and hundreds of thousands of dollars in school fees.

The Athena and Yarralinda schools receive a combined amount of up to $475,000 in recurrent public funding every year to educate fewer than 60 students.

The schools follow the "Way to Happiness" philosophy of Scientology founder L. Ron Hubbard, but maintain they are a secular part of the tax-exempt Applied Scholastics group of schools worldwide, which has strong public links to the church.

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The Way to Happiness Foundation, which distributes a booklet on the philosophy, has been described by former church leader Vicki Aznaran as "a front group to get people into Scientology". US and Australian education authorities have previously complained about Scientology texts being subversively placed in public schools.

At the inner-west based Athena school, listed as the Australian, New Zealand and Oceania headquarters of the Applied Scholastics group, students are funded through a combination of public funding, fees, and tax-free donations, with each of its 30 students benefiting from up to $20,000 in funding per year.

According to MySchool data, the school, which limits class sizes to 15 students, receives just $2000 less per student in public funding than the nearby Newtown Public School, which has been forced to restrict its enrolment boundaries to stem overflowing classrooms.

At the same time, the Yarralinda school outside Melbourne receives up to $11,000 in public funding for each of its 26 students. This is more than the amount received by up to 800 NSW and Victorian public schools, and $2700 more per student than the nearby Rolling Hills school in Mooroolbark.

The public injection to both schools comes on top of the $170,000 in tax-free finance received from other "private sources," including donations from church members to Applied Scholastics emphasised on its own website and more than $470,000 in school fees.

Celebrities including Tom Cruise and John Travolta have long championed the church, which has previously been accused by South Australian independent senator Nick Xenophon, under parliamentary privilege, of torture, perjury and financial coercion.

All of the allegations have been denied by the church.

A spokeswoman for the Church of Scientology said the church does not manage the schools, nor are they a front group for the church.

"[They are a] completely independent secular association which was founded by a group of concerned parents who wanted to educate children," she said.

The principal of Yarralinda, Christel Duffy, said the level of government funding received by the school reflected its educational need.

"There is nothing unusual in any school in any sector raising additional funding, including through donations, to meet the needs of its students," she said.

"Our educational philosophy is clearly and prominently declared on our website and other information material."

While the Athena and Yarralinda schools have maintained low student numbers, the church has been busy establishing an "Ideal Advanced Organisation and Continental Base for Australia and the Asiatic region," according to its global leader, David Miscavige.

In 2010, a church spokesman told ABC's Four Corners there were "tens, if not hundreds of thousands" of members in Australia. However, only 2163 people listed themselves as Scientologists in the 2011 census.

Planning documents approved by Willoughby Council reveal the $57 million super-worship centre on Sydney's north shore will host up to 500 people where senior ministers will be able to train and attempt to cross Scientology's "bridge to total freedom."

A spokesman for the NSW Department of Education said state funding levels recognise the level of resources available to each school based on fees, charges and parent contributions.

"The NSW government per student funding provided to non-government schools, including Athena, is significantly less than is provided to public schools on a per student basis," he said.

In a statement, the federal Department of Education declined to comment specifically on the schools but said Productivity Commission data shows that, on average, total government funding for a student going to a public school is over $16,000 per year, while the support for a student attending a non-government school is $9300.

"Under the Australian constitution, the Commonwealth has no specific power in relation to schooling and does not have a direct role in the registration, administration and operation of schools," the statement said.

The Athena school was contacted for comment.