The principal of an elite Sydney private school has apologised for any confusion or hurt feelings caused by a letter from the school to government asking to retain the power to expel LGBT students and sack teachers.

Last week, it was revealed 34 Anglican schools had signed a letter to the federal education minister asking to preserve a clause in the Sex Discrimination Act that allows religious schools to discriminate on the basis of sexuality and gender.

The clause means they could legally fire teachers for being gay.

In response, thousands of current and former students as well as parents have been writing letters and signing petitions of protest.

On Wednesday, it was revealed two Anglican schools, Abbotsleigh and Barker College, have apologised for the hurt caused by the letter.

Less than a day later, a third school head has apologised. St Andrew's Cathedral School principal John Collier told Hack the letter was written in a "vast hurry".

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"I agree it could have been better expressed," he said.

"People have picked up something and run against the clear intent of the letter.

"I've been talking to people by email and in person ever since to clarify what it's about to apologise for any confusion and hurt feelings.

"That's not what it's about and it's a barrier to getting the message through.

"If you were hurt by this that's not our intention.

"Please be assured schools are not homophobic and not trying to exclude gays - it's not trying to take a stand in this whole arena at all."

The letter from the Anglican Church Diocese of Sydney was written about two weeks ago on October 25 in response to Prime Minister Scott Morrison's statement that schools should not be able to expel students based on their sexuality.

That statement was a response to the Ruddock review recommending the Commonwealth amend the federal Sex Discrimination Act to provide "that religious schools may discriminate in relation to students on the basis of sexual orientation, gender identity or relationship status". This positive right would replace existing religious exemptions in federal law that allow discrimination but do not override state laws.

The Anglican Church letter requests the Sex Discrimination Act religious exemptions - "however clumsy" - stay in place until religious freedoms are legally protected.

"It is essential that a teacher supports the values, ethos and mission of the school as much as he or she can," the letter said.

"It is overly simplistic to state that a teacher merely delivers academic content in the classroom.

"This ignores the powerful mentor and exemplar role all teachers play, and are expected to play, in the education of young people."

Anglican Diocese campaigned against same-sex marriage

Many understood the letter meant the schools wanted the right to ban LGBT teachers.

Rainbow Families NSW, an advocacy group for LGBTI parents and their families, has been spearheading a campaign calling on those who signed the letters to revoke support and make a public statement against LGBT discrimination. It says the response has been huge.

The organisations head of legal, Nick Stewart, told Hack the letter was being understood within the broader context of the Diocese's campaign against same-sex marriage last year.

The Anglican Diocese of Sydney donated $1 million to oppose same-sex marriage, including ads that demonised gay people.

"I don't think that letter can be taken out of context," Nick said.

"That letter encourages its membership to institute the rules within that school according to the religious ethos of the Anglican Diocese.

"I think the Anglican Diocese has made no secret as to what that ethos is."

He said there may not be evidence of schools firing LGBT teachers, but that did not meant they were not being discriminated against.

"We have had and are aware of many teachers working across the school system - in state and private schools - who have experienced homophobic discrimination in their workplaces.

That may not mean being terminated or refused employment but that doesn't mean they're not treated differently in school.

The signatory schools say this is taking the letter out of context.

However, the principals have been reluctant to speak to the media and clarify the intention of the letter.

In early October, Barker College headmaster Philip Heath came on Hack to denounce any school having the right to kick out openly gay students. He said such a thing was "unthinkable".

Two weeks later, Barker College appeared on the list of schools that signed the letter.

Since Friday, Mr Heath has declined Hack's repeated offers to come back on the show and clarify his position and the meaning of the letter.

An apology, but schools still support the letter

In apologising for the hurt caused by the letter, the heads of Abbotsleigh and Barker College did not go as far as to revoke support.

They said the schools did not want the power to discriminate against LGBT teachers, but these legal protections were better than none.

St Andrew's head John Collier took a similar line.

He said the exemptions were "archaic" and "outmoded" and needed to be abolished when federal Parliament reconvened in November.

"We never use it, we didn't ever ask for it," he said.

"We want positive legislation to protect a whole host of freedoms.

"The whole issue has been unhelpfully shaped by some in the media.

There's no evidence anyone has expelled a gay child or dismissed a gay staff member and the whole idea is anathema to any head.

He said teachers were not at school to promote a lifestyle of any kind - apparently contradicting the part of the letter that said teachers were also meant to be exemplars and mentors.

Some Anglican schools refused to sign the letter.

In a letter to parents and students, SCEGGS Darlinghurst principal Jenny Allum said the school welcomed everyone, regardless of sexual orientation.

Ms Allum declined our interview request.