The ACT and South Australian governments could be in weak position when it comes to negotiating over school chaplain funding, says ANU professor John Warhurst.
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By the deadline on Friday the two governments had submitted proposals to keep the funding for the program, hoping they would be able to negotiate so it would include secular counsellors.
Professor Warhurst said, however, that the federal government seemed "quite determined that only religious chaplains will be allowed" and the ball may be in its court.
"With this sort of program, any negotiations would have to be with the states as a group, rather than with each individually,
"Given that the bigger states have already agreed to the terms and conditions, I can't see that the Commonwealth is going to make a different arangement with the ACT," Professor Warhurst said.
The pair are the only governments to campaign against the religious-only aspect of the program, although NSW Education Minister Adrian Piccoli submitted an independent study to the Commonwealth backing the value of secular workers.
Queensland, Western Australia and Victoria have indicated they would acceptthe program as is.
When quizzed on whether negotiating was likely, Scott Ryan, parliamentary secretary to Education Minister Christopher Pyne, said the government "believes in the value of chaplains providing important pastoral care for school communities".
He said he would soon "begin working with the states and territories who have opted to take up the program."
The ACT Minister for Education, Joy Burch, said the territory had a "strong case" to be allowed to use the funding for secular counsellors.
She said she had the backing of the Catholic Education Office and the ACT Association of Independent Schools, which both submitted supportive documents to her letter to Mr Ryan.
The SA Minister for Education, Jennifer Rankine, proposed to Mr Ryan a return to funding for secular workers, asking for an answer from the federal government by September 23.
The ACT and South Australian governments have also been arguing the program cuts pastoral care funding in schools, as set out in the May budget.
"For the ACT, these changes would mean sacking the 23 secular welfare workers currently employed across our public, Catholic and independent schools, and agreeing to a cut to funding of $180,000 a year to ACT schools," Ms Burch said.
ANU professor John Wanna said the federal government may not be able to force the hand of states and territories.
"They will quietly [back down], there won't be a big public embarrassment. I think they will just allow the fund to flow through," Professor Wanna said.