The ACT Government has agreed to take part in the Federal Government's contentious school chaplaincy program on a limited basis.

However, it is not clear if its proposal will get the go-ahead from the Commonwealth.

The High Court upheld a challenge to the program in June, ruling the Federal Government's decision to provide funding directly to chaplaincy organisations was constitutionally invalid.

It prompted the Federal Government to ask state and territory governments to administer the program using Commonwealth funds.

The ACT and South Australia were the last two states refusing to take part in the scheme.

The Federal Government's original offer to the ACT included chaplaincy funding for 47 schools.

Initially, the ACT Government refused the deal because schools could not choose a non-religious counsellor through the scheme.

The Federal Government set an October 3 deadline for a response to its offer and stipulated that all schools should be invited to take part if the ACT participated.

Education Minister Joy Burch has told the Federal Government the ACT was now willing to participate, to prevent non-government schools from being disadvantaged.

"We've put to the Commonwealth a statement saying we are willing to participate to allow the non-government schools access to this chaplaincy funding," she said.

She said the ACT's participation would allow existing public school chaplains to see out their tenure.

"Public schools that are currently not in the program will stay out of the program," she said.

"Schools that have an existing chaplain, that will continue until that position resigns."

ACT will back down if Commonwealth 'plays hard-ball'

But since writing to the Commonwealth on Friday Ms Burch has softened her position and signalled she is willing to accept the chaplaincy funding on the Federal Government's terms.

"If the Commonwealth chooses to play hard-ball then so be it. We'll accept the program but certainly with a level of disappointment," she said.

"I have been very clear now that whilst I wanted both secular and chaplain workers within our schools.

"If the Commonwealth is being very narrow then I will accept that position with disappointment but I am not going to stand in the way of Commonwealth funding flowing to those schools.

"I would hope the Commonwealth clearly sees this as a willingness to participate in the program."

Ms Burch said the ACT Government would also help existing secular welfare workers at public schools.

"The ACT Government does not wish to see people lose their jobs, so will seek to absorb these positions into existing student support programs to the extent that resource constraints allow," she said.

"Once details of the program are finalised the ACT Government will form a cross-sector panel with Catholic and Independent school representatives to select the 47 ACT schools to be funded under the program.

"I look forward to receiving further information on the detail of the program in the form of a draft agreement."

As at May 2014, there were 22 chaplains and 14 student welfare workers placed at the ACT's government schools under the chaplaincy program.

Independent and Catholic schools had nine chaplains, 10 secular welfare workers and one position vacant.

Acceptance into program uncertain

It is uncertain whether the Federal Government will accept the ACT into the scheme, given Ms Burch had not accepted some of the conditions outlined in the original offer.

In a statement Senator Scott Ryan, parliamentary secretary to Education Minister Christopher Pyne, said he was finalising negotiations with the ACT and would make an announcement in the coming week.

“When the Australian Government invited states and territories to participate in the National School Chaplaincy Program, a list of conditions was distributed," he said.

"States and territory education ministers were clearly informed that participation in the program was dependent on acceptance of these conditions."