Schools could be forced to increase fees, scrap programs or cut back on staff as billions of dollars' worth of education funding remains in limbo.

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.

Yet to announce plans: Prime Minister Malcolm Turnbull and Education Minister Simon Birmingham. Credit:Andrew Meares

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.