This leaves the jobs of 25 secular school welfare workers in doubt, with the ACT government saying while it will try to absorb as many as possible under existing school funding arrangements, this cannot be guaranteed.

The federal government was forced to redesign its $244 million National School Chaplain Scheme after the High Court ruled it invalid in June. Under the new arrangements the federal government will fund state and territory governments to administer the scheme.

In August, ACT Education Minister Joy Burch said the ACT would demand secular workers were included and for the existing arrangements funding 56 school welfare workers and chaplains to be continued.

Victoria, WA, the Northern Territory and Tasmania, however, accepted the scheme as is in late September, somewhat scuttling chances of other states to negotiate to include secular welfare workers.

Parliamentary Secretary to the Minister for Education Scott Ryan gave the rest of the state and territory education ministers until last Friday to accept the funding.

Ms Burch wrote to Mr Ryan on Friday saying the ACT would accept the funding and she was "disappointed" the Commonwealth did not agree to the inclusion of secular counsellors.

"Requiring that these schools apply for a religious-based chaplain without the option for a secular worker is inconsistent with the principles in which they are based," the letter read.

In a final effort to limit increased religious influence in public schools, Ms Burch is urging the federal government to not make provision for new religious chaplains to be appointed.

"It is the ACT government's position that...public schools participation will be limited to seeking funding to continue employing individual chaplains already in the program," Ms Burch wrote.

As of May there were 22 chaplains and 14 secular welfare workers funded in the federal chaplain program in ACT public schools.

Mr Burch said the territory would comply with the scheme's condition to form a cross-sector public, private and Catholic school panel to help administer the scheme.

The panel will be responsible for selecting the reduced number of 47 schools to receive religious chaplains.

Twenty-five secular counsellors or welfare workers are in the firing line if they cannot become a chaplain. Fourteen are in the public system, two in the private system and nine in Catholic schools.

The spokeswoman said the ACT Education Directorate will be looking for ways to absorb these secular workers. "We don't want to see them lose their jobs," she said.

In early September Ms Burch said the territory had a "strong case" to be allowed to use the funding for secular counsellors, considering the Catholic Education Office and the ACT Association of Independent Schools both supported her proposal.