But the National Catholic Education Commission has warned the Catholic system remains in an "untenable position" and may be forced to raise fees or redistribute funds from low socioeconomic schools to higher socioeconomic schools in order to neutralise the cuts' impact.

Senator Birmingham has stood by his policy of transitioning all schools to needs-based funding within the next decade. Writing to ACT Catholic schools, he vowed to end the "special deals" that saw Canberra's system receive funding based on an SES of 101 rather than their actual scores, which reach as high as 128.

Senator Birmingham told media on Tuesday that Catholic schools would at least maintain their current funding level "over the next few years".

"We've been clear all along that there were different circumstances in Canberra because the way in which socioeconomic status has been calculated under the old deals of the Gillard Government in Canberra wasn't using Canberra data," Senator Birmingham said on Sky News on Tuesday.

"As we've been clear from day one, some funding was set aside for that and that funding notionally ensures that the Catholic system in Canberra at least maintains its current normal level of funding over the next few years."

Canberra's Catholic system will also have access to an almost $40 million "adjustment assistance" fund open to disadvantaged and vulnerable schools.

Catholic Education Office Archdiocese of Canberra and Goulburn director Ross Fox said the transitional arrangements meant little to ACT systemic schools.

"The way I'd describe it is the minister's policy wants to throw Catholic schools in the ACT off a cliff, we don't want to go over the cliff and we don't appreciate a ladder to get down the bottom of the cliff," he said.

The campaign against the government's proposed funding changes continues with Mr Fox's office compiling a series of photographs for the minister aimed at showing the difference between high-SES independent schools and those in Canberra.

Parents at Rosary Primary in Watson have been warned of significant fee increases and encouraged by community council chairman Patrick McArdle to write to the government against the policy which he said sought to "divide and denigrate".

Separately, the National Catholic Education Commission has written the only way to avoid fee increases would be to redistribute money away from the Catholic schools set to receive funding increases.

"It will necessitate redistributing away from some lower SES schools to higher SES schools and/or increasing fees substantially in man schools," its submission to the Inquiry into the Australian Education Amendment Bill said.

"By publicly suggesting, however, neither of these two remedies is acceptable, the government has left Catholic schools in an untenable position."