The Federal Government has announced changes to its school chaplaincy program to get around a recent adverse High Court decision.

In June, the court upheld a challenge to the National School Chaplaincy Program, saying providing funding directly to chaplaincy organisations was constitutionally invalid.

The main question examined in the case was whether the executive government had the power to fund such programs directly through local organisations.

As a result, the Government has now decided to ask state and territory governments to administer the program using Commonwealth funds.

If they agree, the $250 million program - to run over four years - will remain open to chaplains of any faith as long as they do not attempt to convert students.

"The Government believes that school chaplains make a valuable contribution to the wellbeing of students and school communities," parliamentary secretary to the minister for education, Scott Ryan, said in a statement.

WA Education Minister 'supportive' of proposal

Western Australia's Education Minister Peter Collier is confident the state's Cabinet will agree to administer the school chaplaincy scheme.

WA already operates its own scheme and Mr Collier said he supports the Federal Government initiative.

"But as with all decisions, it must go through the correct processes and that's exactly what I'll do," Mr Collier said.

"We're supportive of any additional funding and if that comes from the Federal Government, we'll be delighted.

"Quite frankly, the reason that [the funding] was under threat was more of a technicality as opposed to a commitment from the Government."

The South Australian Government said it would consider the proposal if the Commonwealth reinstated provisions allowing for funding to also be used to engage secular social workers.

The Tasmanian Government said it wanted more detail before considering it would consider the Federal Government's request to administer the program.