Prime Minister Malcolm Turnbull has played down a Victorian government decision to go it alone on the controversial Safe Schools anti-bullying program.

Victorian Education Minister James Merlino has confirmed on Twitter there will be no changes to the program in Victorian schools after the federal government's "total cave-in to bigots".

No changes to Vic safe schools program in wake of Turnbull Govt recommendations - total cave-in to bigots. We know #safeschools saves lives. — James Merlino (@JamesMerlinoMP) March 18, 2016

"The Victorian government obviously can fund whatever programs it wishes," Mr Turnbull told reporters in Sydney.

The federal government unveiled changes to the program on Friday after an independent review found some lessons and content were inappropriate for children.

As a result, program materials - such as those titled "OMG I'm Queer" - will be now be limited to secondary schools.

Lesson plans that make children role-play scenarios about switching gender will be cut.

A chorus of conservative federal government backbenchers led the revolt against the program which focuses on gender diversity and same-sex issues.

related reading 'I remember people throwing food at her': project shows need for Safe Schools program

Mr Merlino told the ABC the program saved lives and Victoria would continue to expand it into every government secondary school in the state.

The state government will also chip in extra money if Canberra pulls funding.

Opposition Leader Bill Shorten said conservatives in the Liberal Party had bullied Mr Turnbull until he caved in.

"I would rather trust the teachers and principals of Australia's schools than the right-wing of the Liberal Party with the welfare of Australia's children," he told reporters in Melbourne.