Ms Berry's caution came after Brindabella Christian College asked parents to vote no in the postal survey on same-sex marriage with a warning the school may no longer be able to teach Biblical views on marriage and family should the Marriage Act change.

Ms Berry said: "Of course school leaders, staff and parents and carers are free to hold their views on marriage equality but this cannot be allowed to occur in a way that damages the welfare of young LGBTIQ+ people."

Mr Abbott slammed Ms Berry's reminder as "a pretty outrageous interference with freedom of speech and freedom of religion".

"If that's the way the school thinks, why can't it speak its mind," he said on 2GB.

"If Woolworths and Qantas and these companies can speak their mind without anyone bullying them, why can't the Brindabella Christian College speak its mind and give its advice without being bullied by the ACT government?"

Mr Abbott said Ms Berry's comments showed the dangers to religious freedom should same-sex marriage be legalised.

"Obviously if the yes vote gets up it will be the supporters of same-sex marriage who will then have the signed blank cheque to fill out and you just can't trust these people given the way they're conducting themselves ... now to ensure that these protections are there," he said.

Ms Berry said her message was about welfare for students.

"Mr Abbott might not feel any duty of care to Canberra's young people but I do," she said.

"It's a simple message to all in our school community to put the welfare of students - often those who don't have a voice in debates like this - first."

Brindabella Christian College principal Bruce Handley sent his four-page statement on same-sex marriage home last week.

He argued there was no promise of protection for religious freedom should the vote go through.

"There simply is no certainty around what legislation may be proposed, a YES vote is basically signing a blank cheque to the Parliament to proceed with changes," he said.

Other Canberra schools, including Christian and Islamic campuses, have either encouraged parents to participate in the survey, shared their position without explicitly encouraging a yes or no vote or stayed out of the debate.

Ms Berry urged ACT schools to remember the diversity of their students and staff.

"Our diversity is beautiful and children should be encouraged to be themselves without experiencing prejudice," she said.

"All schools have a duty to provide a safe, respectful and inclusive environment free from bullying, harassment, discrimination and violence."

Ms Berry, who supports same-sex marriage, will soon launch the ACT's answer to Safe Schools. The Safe and Inclusive Schools Initiative will aim to support lesbian, gay, bisexual, transgender and intersex students.

"The Safe and Inclusive Schools Initiative will be available to all ACT schools, government and non-government run, who seek access to it," she said.