With many public school administrators facing the threat of heavy budget cuts from the federal to state level, Education Minister Christopher Pyne has assured private schools that the Federal Government will continue funding them directly.

Private schools had been concerned they would have to increase their fees under new funding arrangements, which link funding amounts from 2018 with the consumer price index.

The CPI-based increase will be about 2.5 per cent per year, around half the rate of increase promised by the previous Labor government.

Independent Schools Queensland says in real terms, it is a cut.

“This could lead only to a reduction in programs and education quality or, in the case of independent schools, significant increases in fees,” executive director David Robertson wrote in The Australian on Wednesday.

Mr Robertson argues that using CPI does not reflect special costs schools face including implementing the national curriculum or salary adjustments.

Some schools say there should be a education-based measure for the amounts and increases in school funding.

Meanwhile, speaking at a Christian schools forum, Pyne said he wants to maintain direct funding of private schools by the commonwealth, which has occurred since the nineteen-sixties.

It contradicts the suggestions from the recent Commission of Audit report, which suggested the Federal Government withdraw from funding schools entirely, distributing money to states and territories to hand out.

“I am not attracted to that model,” Pyne told the forum in Canberra.

Another key piece of funding to benefit private schools in particular has received criticism this week.

The school chaplaincy program’s $245 million funding increase continues to be questioned, with non-religious groups arguing it could be spent on formal counselling or disability assistance, rather than spiritual guidance and religious education.

One of the main Christian groups providing chaplains to schools says the funding boost has brought it into profitability for the first time in several years.

Access Ministries acting chief executive Dawn Penney says the group expects to be able to spread the fine moral lessons of the Bible in many more classrooms, with its latest $5.7 million funding grant.

“We expect all of our current schools to be able to reapply for funding, along with even more schools as the program is so highly valued by school communities,” she said.

Australian Education Union Victorian branch deputy president Justin Mullaly has told Fairfax reporters that the program no longer allows non-religious welfare staff.

He said many schools did not have a single dogmatic lean, and the broader scheme allowed the hiring of staff relevant to more of the student body.

“Often that was in the form of a social worker or psychologist,” he said.

“It allowed schools to get the professionals they needed.”

He said the money allocated to Access Ministries alone could hire 50 full time teachers.

A High Court challenge to program is underway in Queensland, which reports say may affect the direct relationship with private schools.