Ross Fox, head of the Catholic Education Office in the ACT, said schools had been struggling in the wake of cuts to the non-government sector unveiled last year, with many considering scaling down, hiking up fees or closing their doors altogether.

"We [were going] to lose in excess of $300 million over three years here in ACT Catholic schools, we were really the most hard hit in the country," Mr Fox said.

"Fees would have had to increase by multiples, some were thinking of closing."

The new cash injection, designed by the Morrison government to end the school funding wars after sustained lobbying from the Catholic sector, is expected to restore about $220 million to Canberra's Catholic schools over the next decade.

At the Association of Independent Schools of the ACT, executive director Andrew Wrigley could not yet give an estimate on what private schools would likely take home from the deal, but said they would be "fine".

While the package does not include any new money for public schools, a key win for the ACT's non-government sector was a change to the way private schools will be funded from 2020.

Currently, census data is used to access the socioeconomic status of schools, and so determine their share of funding under the needs-based Gonski model. Now, for the first time, parental income tax records willdecide funding.

"With the salt and pepper approach to public housing that's historically happened in the ACT, and [disadvantage] spread out more, that [census] data was most flawed in Canberra so we've been vindicated on this," Mr Fox said.

A new $1.2 billion fund also will help Catholic and low-fee independent schools stay affordable as private schools transition to reduced funding under the Gonski 2.0 model, which will see them receive 80 per cent of the school resourcing standard from the federal government. Labor has labelled the pot of money a "slush fund".

Some of Canberra's private schools are funded up to almost 150 per cent of the standard, and special deals were struck with the ACT non-government sector last year to help prop them up during the transition.

Both Mr Fox and Mr Wrigley said they had been reassured those funds would not change as a result of the new deal.

"We've still got that $36 million until [2027] to help us [become] more efficient and help schools adjust," Mr Fox said of the ACT Catholic school system.

"We support a well-funded government school system but it's not a zero-sum game. You can't have 35 per cent of your revenue disappear [as we did] and expect nothing to change."

The Australian Education Union, including its ACT branch, has called on state and territory ministers to reject the funding package as it fails to reinstate previous cuts to public schools.

On Friday, ACT Education Minister Yvette Berry joined her NSW counterpart Rob Stokes in calling for sector-blind school funding, but did not say whether or not she would rule out supporting the deal.

While Ms Berry acknowledged census data had always struggled to reflect the true need in the ACT's diverse suburbs, she said she had "moved quickly" to lift the ACT's contribution to the non-government sector when it fell short of the territory's share of the resourcing standard.

Public funding for private schools should fall below money for government schools "in line with the capacity of parents to pay fees and their choice to seek private and religious education", she said.

Chris Watt at the Independent Education Union said most schools, both public and private, would not get the money promised for 2018-19 under the deal, which locked in unreasonable limits on staff salaries for at least the next five years.

The federal minister for education Dan Tehan has been contacted for comment.