Prime Minister Scott Morrison has struck a multi-billion dollar peace deal with Catholic and independent schools.

The $4.6 billion package over a decade brings to an end a long-running war over the Gonski 2.0 school funding model.

"For students, this will mean the opportunity to get the best results from school. For parents, it will mean that choice remains affordable," Mr Morrison told reporters in Canberra on Thursday.

"For teachers, it will mean certainty of funding so they can get on with the job."

The government will chip in $3.2 billion over 10 years from 2020 to fund changes to the way parents' wealth is measured, based on income tax data.

A $1.2 billion Choice and Affordability Fund over 10 years will help keep fees affordable and maintain choice.

In 2019 independent and Catholic schools will receive $170.8 million over the calendar year.

Labor claims it will lead to an overall cut of $17 billion.

"What the Prime Minister is saying is if you send your kids to Catholic school that's fine, we'll give you extra funding, but if you send your kids to public school - too bad - you're on your own," Labor's education spokesperson, Tanya Plibersek, said.

The deal brings to a head months of discussions with the National Catholic Education Commission (NCEC) and Independent Schools Council of Australia (ISCA).

"We commend the new Education Minister Dan Tehan for recognising that the 2017 changes had jeapordised the future of low-fee, low-expenditure schools in areas where they've served families for generations," NCEC Acting Executive Director Ray Collins said.

While the ISCA says the announcement will bring certainty in the short term.

"ISCA recognises that there is much more work to be done to enable the full implementation of the new methodology, to be phased in over ten years," it said in a statement.

"The Independent sector will continue to work closely with the Government and the Department of Education and Training on this important work."

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Mr Morrison had a clear message to any parents of state school students frustrated with the costly side deal struck with private institutions.

"I don't think parents will be cynical like that. They will know that we're funding public schools at record levels," he said.

"All parents want to have choices about how they educate their children, and where there are issues that need to be addressed, we'll address them."

Mr Morrison said where the money was coming from would be set out in the mid-year budget review due in December.