The territory's most expensive private school fees will exceed $27,000 for the coming school year while, in the Catholic sector, the Archdiocese of Canberra and Goulburn said it had been forced to put up its own centrally-controlled tuition fee by about seven per cent rather than the usual three to four per cent rise.

Over the next decade, all schools in Australia will have their funding adjusted according to a cross-sector, needs-based formula introduced under the Gonski reforms, known as the Schooling Resource Standard. That will see a number of over-funded non-government schools lose money but many cash-starved public schools topped up.

On Tuesday, the ACT government told The Canberra Times it would introduce cuts along the same lines to non-government schools over the next five years as part of its commitment to equitable funding.

Andrew Wrigley from the Association of Independent Schools of the ACT said this year's fee increases went beyond keeping pace with rising operational costs; schools needed to get their business models in order.

At the ACT Catholic Education Office, Ross Fox estimated parents would pay on average about $185 more for a primary school student and $430 for secondary in 2019, once local school fees were added into the mix. That will push the average price of a Catholic education in Canberra, generally the more affordable non-government option, above $6000 a year for secondary and close to $3000 for primary.

"We've tried really hard not to increase fees too much, we don't want any family missing out due to financial hardship," Mr Fox said.

"But we thought this was the prudent thing to do, better to go up a little now than be [unprepared] for cuts down the line."

Mr Fox said a small number of under-funded Catholic schools would gain funding under the new federal model, but most were bracing for cuts.

A spokesman for the ACT government estimated its own plans to introduce the model would have a relatively small impact on the sector, at between $4 and $7 less per student in 2019. The territory already funded Catholic schools "well above" its 20 per cent share of the standard, he said, and non-government schools would continue to see year-on-year increases in funding, as well as have a share in the territory's $15 million school infrastructure fund.

But Mr Fox said, by its fifth year of operation, up to $1000 per student could be lost in territory funding under the model, with Catholic schools appearing to be the hardest hit.

"It assumes parents can just pay more fees," he said.

Mr Wrigley said non-government schools had a large footprint in the ACT, already saving the territory money on public education.

While two private schools had yet to release their 2019 fees on Tuesday, an analysis of those that had revealed some of the sharpest increases would be felt at Marist College, where fees were rising about seven per cent, and at Canberra Girls Grammar, which would charge an additional $1200 for a senior student.

Some schools, such as Marist and Catholic school Merici College, listed all-inclusive fees but many fees did not cover extra costs for excursions, camps and certain subjects.

Canberra Grammar School will remain the territory's most expensive this year, charging about $1000 extra for a senior student at $27,775.

A spokesman said the school did not offer discounts for families on lower incomes, as did a number of other schools such as Trinity Christian, but it did offer a range of scholarships. This year the school awarded six scholarships to Indigenous students entering Year 11, and boarding places would be set aside for students on the south coast through a new partnership with Indigenous education charity the Podmore Foundation.

But, fees aren't going up everywhere - the Islamic School of Canberra has charged $2450 since 2017 and Canberra Christian School is keeping its own fees at 2018 levels, after some rigorous reshuffling of its budget.

Principal Bree Hills said the school catered to a number of middle income families and only put up fees as a last resort.

"It's a stretch for them sometimes on what we already charge, let alone putting it up so we always look at [our budget] first," she said.

"But there are some years when you can't do it and you [have to increase fees] and I understand that too."

Mr Wrigley said private schools had anguished over fee increases this year, mindful of their impact on the community, and were working to bring expenditure down.

While federal cuts come with help from a special transition fund, he said the change could impact unfairly on a single generation of families unless schools planned accordingly.

Peter Goss at the Grattan Institute backed the move towards consistent, needs-based funding but noted a boom in Canberra's population would likely put pressure on schools

"That could be driving up fees," he said.

Wage growth in the sector had also been slightly above average, he said.

This year the Canberra Montessori School raised its membership fee from $60 to $120 for the first time in 15 years, but staff said most of its tuition fee hikes reflected salary increases.

Mr Fox said Catholic schools offered generous discounts for families with more than one child and had policies to waive fees for those who could not afford to pay them.

In 2018, more than 37 per cent of Canberra students attended a non-government school, though the public sector has been gaining numbers in recent years.