With the so-called Gonski funding agreement due to expire at the end of the year – and the Turnbull government yet to announce what will replace it – public and private schools have warned that months of uncertainty is taking its toll on their ability to plan their budgets.

Magpie Primary School, a small rural school on the outskirts of Ballarat, is preparing to lose two teachers next year due to the funding uncertainty.

Principal Peter Clifton said these teachers ran a successful literacy and numeracy program, which had been funded through the Gonski agreement but was now at risk.

"The program has had an enormous impact," he said. "Every prep and grade one student now sits above the national benchmark in literacy and numeracy. We are above average and we want to stay that way."

The anxiety has also spread to the Catholic and independent school sectors, which are warning of fee hikes and program cuts if any future arrangement resulted in some private schools having their funding growth curtailed.

Such concerns intensified earlier this year, when it emerged that the Commonwealth was examining how to pull back the generous annual funding increases locked into legislation by the Gillard government.

While federal Education Minister Simon Birmingham insists funding won't be cut in real terms, Independent Schools Victoria chief executive Michelle Green said some principals had put their planning on hold as they waited for Canberra to provide some clarity about how it would resource them over the next few years.

"Any sudden funding changes could result in unanticipated fee increases that many families and school communities will not be able to manage," she said.

Catholic Education Melbourne executive director Stephen Elder also warned that Catholic schools would consider cutting programs or increasing fees if the federal government abandoned its promise of annual school funding increases of 3.56 per cent.

"This could have a significant impact on families and on some programs, including fee relief subsidies for disadvantaged families or our initial teacher training programs," he said.

Canberra has long made it clear that it would ditch the fifth and sixth years of Labor's signature Gonski needs-based approach and replace it with a more nationally consistent agreement.

The Commonwealth had promised to finalise plans at a Council of Australian Governments meeting that was meant to take place earlier in the year, but was pushed back to June to accommodate premiers who couldn't attend – including Victoria's Daniel Andrews.

As a result of the delay, Victoria's own plans for a schools shake-up appears to have stalled. Last year, a funding review by former Labor premier Steve Bracks found that the Commonwealth's decision to renege on the last two years of Gonski could cost Victorian government schools around $1.1 billion. What's more, the review found, unless this decision was reversed the state would be forced to rethink its own funding regime in a bid to negate the impact.

But while state Education Minister James Merlino conceded in September that a rethink was needed – and said further details would be provided at this year's May budget – his spokesman told The Sunday Age last week: "We can't make informed decisions without knowing what the Federal Liberals are planning to do."

Mr Birmingham hit back on Friday, saying it was hypocritical for Victoria to demand precise details of federal funding "which they already know will grow from existing record levels, when they won't even outline their own scale of investment".

"The Turnbull government has consistently said that future schools funding arrangements would be concluded at the first COAG meeting of this year and that remains the timeframe we work toward," he said.

Australian Education Union Victorian branch president Meredith Peace said Gonski had been used to provide extra support and programs "and that has meant new staff have been employed. With no certainty, people's employment is in jeopardy."