In a majority decision earlier today, the High Court decided funding for the chaplaincy program was unconstitutional because of the payment method used - not because of religious reasons.

The challenge was brought by Toowoomba man Ron Williams, who objected to what he described as a "religious missionary" being put into schools, and pointed to constitutional restrictions on any Commonwealth officers being subject to a "religious test".

While the court dismissed that aspect of the case, the ruling has a wide range of implications for how the Federal Government funds different programs.

Attorney-General Nicola Roxon says the Government has been doing "contingency planning" in the lead-up to today's ruling, and is confident it will find a way to keep chaplains in schools.

"We are committed to both the program and the funding for the school chaplaincy program...and there are different ways that we will be able to provide for the program and the funding to continue," Ms Roxon said.

"It is clear that there is a cure for each of these problems that are identified [by the court] - whether it's particular legislation, whether it's payments through the states, whether it's other sorts of contingency steps that can be taken."