Parents of Canberra's Catholic primary school students will fork out up to $5000 a year more in fees under the government's planned funding changes, new modelling shows.
But Education Minister Simon Birmingham has rejected the estimate, saying it was based on "fundamentally flawed" models.
Catholic Education Office Archdiocese of Canberra and Goulburn released the figures on Sunday showing the ACT's 21 Catholic primary schools would have to increase fees by at least $1000 for each child per year if the government's school funding reshuffle proceeds.
Fee hikes would reach more than $5000 for two schools, St Thomas More's Primary School, in Campbell, and St Bede's Primary School, Red Hill, under estimates that compare expected fees under the Coalition's proposed needs-based model with net recurrent fees that exclude money raised for capital costs.
Parents face fee surges of at least $3000 at another four schools, Sts Peter and Paul Primary School, Garran, St Joseph's Primary School, O'Connor, Holy Trinity Primary School, Curtin and St Jude's Primary School, Holder.
Catholic Education Office Archdiocese of Canberra and Goulburn director Ross Fox said it feared the funding changes would put low-fee Catholic school education out of reach for many families.
"I believe parents would be incredibly concerned if the government was pursuing a policy resulting in these fee increases," he said.
Senator Birmingham said the group's modelling and claims were misleading, and that funding for ACT Catholic schools would grow by $2 million over the next four years.
The government will provide an additional $300 million over the next 10 years for non-government schools' capital infrastructure, on top of the existing annual allocation that in 2016 was $140 million.
"I am committed to stopping the school funding wars and I urge all parties to end their scare tactics and stop their campaigns for special treatment," Senator Birmingham said.
Catholic School Parents of the Archdiocese of Canberra and Goulburn chairman Paul Compton said members had expressed anger about the government plan.
"We will be pushing fairly hard for those decisions to be changed," he said.
Schools would have to expand class sizes and lower the quality of teaching if they opted not to hike fees, Mr Compton said.
The ACT's non-government sector is the only in the nation to definitively lose out under the policy proposed by Prime Minister Malcolm Turnbull and Senator Birmingham last week.
Tuesday's budget will include an extra $2.2 billion extra for schools over the next four years on top of the $1.2 billion announced in last year's budget, but the new policy will involve a substantial shuffling of funds between the states and different school sectors.
Under a special deal struck by the former Labor government, the ACT's Catholic schools were funded according to an allocated socioeconomic score of 101 despite many measuring above that.
It is understood the new policy will scrap this deal, and funds provided to all Catholic and independent schools in Canberra will be reduced over the next decade.
The Catholic Education Archdiocese of Canberra and Goulburn will hold a meeting about the changes at St Clare's College, Griffith on Monday, May 8 at 6pm.
- With Emily Baker