It comes a day after federal Education Minister Simon Birmingham began talks with his state and territory counterparts on a new four-year school funding model, which would begin in 2018 and replace Labor's Gonski agreements.

Australian Education Union Victorian branch president Meredith Peace said Victorian schools needed funding certainty from the Andrews government, regardless of the Turnbull government's position.

"We want the state government to fund years 5 and 6 no matter what happens," she said.

This is when the bulk of the Gonski money was meant to flow to Victorian schools.

According to a report by the Auditor-General, the original six-year deal would have provided Victorian schools with about $4 billion of Commonwealth funding and $3.2 billion of state funding during the final two years.

"Victorian schools can only deliver programs that will help our children in the long term if they have the funding certainty Gonski needs-based funding will provide," Ms Peace said.

Education Minister James Merlino has accused the Turnbull government of short-changing Victorian schools by $1 billion but has refused to commit to the full deal. He said future funding would be considered ahead of the budget.

Meanwhile, the New South Wales government has promised to fund the entire agreement, with its fiery Education Minister Adrian Piccoli declaring a "war on fairness" and accusing the federal government of deserting public schools.

Acting Education Minister Jenny Mikakos, who attended the talks on Friday in Mr Merlino's absence, said she would continue to fight for the full Gonski funding.

Victorian Association of State Secondary Principals president Judy Crowe said it was difficult for schools to plan programs and employ permanent staff without funding certainty.

But she raised concerns about the flawed implementation of the Gonski panel's recommendations, particularly the promise that "no school would be worse off". She said this meant the money was not distributed fairly, with wealthy private schools continuing to receive generous government subsidies.

She said the federal government needed to address this issue with any new school funding model.

The Lakes South Morang P-9 School principal Kerrie Heenan said a there was "significant disappointment" in schools because the state and federal government had not committed to the entire deal.

"If we are about a fair go for all kids and want to give them an opportunity to be what they want to be we need to stop putting dollars into private schools and put them into schools like mine where the dollars will make a real difference," she said.

Mr Birmingham believes the current school funding arrangements are a "corruption" of David Gonski's original vision. He said the patchwork of "special deals" with states must be replaced by a simpler, fairer model.

He hopes to present state and territory education ministers with a final school funding proposal in the first half of 2017.

Victoria's state school students continue to receive the least government funding in the country. The most recent data shows that each state school student received $2253 less in state and federal funds than the national average in 2013-14.