Prime Minister Julia Gillard said this week that Canberra's schools would lose about $40 million if a Coalition government failed to implement the proposed Gonski funding reforms.

But opposition education spokesman Christopher Pyne subsequently wrote to Chief Minister Katy Gallagher to warn her that ACT schools would be $38.5 million worse off under Labor's plan.

"In terms of your state our analysis reveals a $38.5 million reduction over three years for school educations in the Australian Capital Territory when comparing the 2012-13 Federal Budget to the 2013-14 Federal Budget,'' wrote Mr Pyne.

Mr Pyne also warned that many ACT schools could receive a lower rate of Commonwealth funding indexation in the future because they were above the proposed national school resource standard.

Negotiations between the federal and ACT governments on how much funding Canberra schools would receive under Gonski are continuing.

Ms Gallagher dismissed Mr Pyne's claims about ACT schools losing funding under Gonski as "rubbish''.

"Basically they're just not true,'' she said. "Those are not the figures we are working around - I can confirm that.

"And I can confirm the negotiations we are having with the Commonwealth are about having extra money coming to education in the ACT, not a cut of $38.5 million, which is what he seems to be alleging.''

ACT opposition education spokesman Steve Doszpot said a lack of certainty over future funding was making it difficult for local schools to budget.

"I'm calling on the Chief Minister to stop the uncertainty, give us an indication as to what we can expect, what the education system can expect - both the government and the non-government sectors,'' Mr Doszpot said.

Ms Gallagher said a funding agreement needed to be finalised with the Commonwealth before present arrangements expire at the end of next month, and preferably before the territory budget is announced on June 4.