The Turnbull government had ordered a review of the program – aimed at reducing bullying of gay, intersex and gender diverse students – in response to pressure from the party's conservative wing, led by Cory Bernardi and George Christensen.

In response to the review, the government said it would reduce lesson content, restrict it to secondary schools, move it to a government website, remove links to third party groups and require schools to get parental consent before using its materials.

But the ACT's education minister Shane Rattenbury said on Sunday while he was open to some changes, such as giving more information to parents about the program, it was unusual for schools to seek permission from parents before running programs.

"Secondary schools do not seek individual parental permission for students to access lessons on health, sex education or other kinds of peer support – they should not need to seek individual permission to have access to an anti-bullying program," he said.

"The Safe Schools program supports a school culture that is happier, safer and more inclusive for all young people. Young people of all ages should have access to a program which supports young people dealing with their sexuality at the time that they need it."

On whether the program would continue to run in the territory's primary schools, the ACT government said it still had to review the proposed changes.

The Victorian government has said it will not make any changes to the program following the federal government review.

Queensland backbencher George Christensen likened the program to grooming from sexual predators and described it as putting children at risk of being sexualised at an early age.

It was these comments in part that led chief minister Andrew Barr to make a strong defence in ACT parliament earlier this month of the program and of LGBTI children.

"Our message to LGBTI kids [is] that they are fine, we support them and there is nothing wrong with them and don't let any Neanderthal conservative tell you anything otherwise," he said.

In Canberra, there are about 23 public schools – about a quarter of schools – and one independent school which had joined the program, Mr Barr said.

Minister Rattenbury said the ACT government fully backed the program and would financially support it should the federal government withdraw funding.

He said the decision to review Safe Schools was about the "ideology of the hard right wing of the Liberal Party", and he estimated the ongoing costs of the program in the ACT to be in the tens of thousands of dollars.

"It's a disgraceful irony that the Federal Government chose the National Day of Action Against Bullying and Violence to announce that it would gut a successful anti-bullying program that helps to make our schools a safe environment for our young people.

"The program is being run successfully in ACT schools, and is greatly valued by students, educators, parents and the broader community.

"Given that one in five transgender young people experience physical abuse and one in three consider suicide, it's a program than can potentially save lives."

Shadow minister for education Steve Doszpot has previously supported the review, saying some of the material linked to the program was questionable.