More than $1 billion in federal funding to South Australian schools is now in limbo because of a deepening stand-off over the Federal Government's Gonski 2.0 education plan.

Just weeks out from the end of the school year, SA Education Minister Susan Close has written to her federal counterpart Simon Birmingham indicating the SA Government will not sign an interim funding agreement.

Education Minister Susan Close is holding out for a different deal for SA. ( ABC News )

The federal plan includes $1.285 billion set aside for SA schools in 2018, with funding due to increase each year over the next decade.

But the SA Government said South Australian schools would be $210 million worse off over the next two years.

"South Australia's public, Catholic and independent schools are also being held to ransom by the Federal Government, which has threatened to withhold $1.2 billion in funding," Ms Close said.

"I want to work constructively with the Federal Education Minister on a future agreement but I absolutely refuse to be complicit in $210 million being withheld from South Australian schools."

In May, Prime Minister Malcolm Turnbull announced the overhaul known as Gonski 2.0, promising a needs-based system to determine education funding across the country.

But the plan has been criticised by education groups and some state governments, who said it would lead to major cuts.

"Without the original Gonski agreement in place, all three schooling sectors in South Australia would suffer a massive financial loss," Ms Close said.

But Mr Birmingham has accused the SA Government of attempting to "bully" the Commonwealth and putting politics ahead of education outcomes.

"By refusing to sign this agreement state Labor is effectively saying we don't want $1.29 billion for SA schools next year, which I'm sure is at odds with school communities across the state," he said.

"Jay Weatherill's constant desire to have petty political fights with Canberra is jeopardising a federal funding boost to South Australian schools of $804 million."

Mr Birmingham said Productivity Commission data showed SA Labor had slashed "$56 million from government schools" at a time when federal funding was rising.

"The Turnbull Government will never let Australia go back to the 27 special schools funding deals Labor stitched up that the Weatherill Government is trying to bully us back into," he said.