The Association of Independent Schools of the ACT said it was not yet certain what share of new federal funding would flow through Canberra's 17 independent schools catering to nearly 14,000 students, as they moved onto the Better Schools Plan.

But executive director Andrew Wrigley said new federal Education Minister Bill Shorten had been "decisive" in dealing with ongoing concerns from the independent schools sector that they could have been disadvantaged under the new funding regime.

Last month's ACT budget included new and vastly increased funding for all of Canberra's schools, following the ACT signing onto Gonski in May. But the budget also revealed Catholic systemic schools in the ACT were slated to receive almost twice the amount over the life of the agreement than independent schools due to the deal.

While Canberra's government schools are set to receive the biggest slice of the Gonski pie at $347million by 2019, Catholic systemic schools will receive an additional $59million, compared with $30million for independent schools.

That $30million figure is now expected to rise by millions of dollars in additional assistance over the six years of the funding agreement.

Mr Wrigley said the deal was in its final stages of being signed off on by independent schools. "It became apparent several weeks ago that a separate deal had been offered to ACT systemic Catholic schools, providing a means of additional funding in recognition of the unique demographic characteristics of schools in the ACT," he said. "This meant that ACT non-government schools ... were being treated differently."

Mr Wrigley said Wednesday's deal "now assures that ACT independent schools will receive a similar quantum of additional funding to that offered to ACT systemic Catholic schools".