Proponents of the school chaplaincy program are urging the ACT to accept Federal Government funding for a revamped national scheme.

The school chaplains program was introduced by the Howard government in 2006.

But this year it was challenged in the High Court and found to be invalid, as it went outside the Federal Government's funding powers.

The High Court decision prompted the Abbott Government to attempt to fund the scheme through the states and territories, however the ACT and South Australia said they would not cooperate.

ACT Education Minister Joy Burch said she wants the chaplaincy program to continue in its current format, where schools can choose between a faith-based chaplain and a secular counsellor.

But National School Chaplaincy Association Peter James said schools that want a chaplain should not be denied one because of ideology.

Mr James said in the ACT there were more than 30 schools that, through a process of community consultation, had chosen to have a chaplain.

"Our question to the ministers in those states and territories is how is anyone's interests served by denying those schools their choice?" he said.

"They find the service a valuable one so why deny them that simply because somebody misses out? It means everybody misses out and that seems no solution to the problem."

Mr James said a chaplain was an additional resource within a school's existing pastoral care team and several university studies have shown school communities found them a valuable resource.

The Federal Government has set a deadline of this Friday for the ACT to accept the funding.