FEDERAL Attorney-General Nicola Roxon says the national schools chaplaincy program is the only one at risk from a landmark High Court decision handed down today.

A majority of the court today ruled payments from the Commonwealth to Scripture Union Queensland (SUQ) to provide chaplaincy services were invalid.



The High Court said executive power as defined in section 61 of the Constitution did not empower the Federal Government to enter a funding agreement to make the payments.



The decision raised concerns all such government programs were affected but Ms Roxon denied this.



"The only government program that was challenged and invalidated by this decision was the National School Chaplaincy Program," Ms Roxon said in a statement.



"The Government is committed to maintaining funding for important community programs."



About 3700 schools around the country have chaplains or student welfare workers funded under the current arrangements.



Ms Roxon said there were contingency plans in place for commonwealth funding and the Government was reviewing the judgment to determine if there were any wider implications.



SUQ said the ruling was only about "a particular historical funding model".



"Even though that model might be invalid, it does not keep chaplains from supporting school communities," a spokesman said in a statement.



"Instead, it means that a new funding model is needed."



The Atheist Foundation of Australia called the decision a victory for democracy and secularism in public schools.



However, High Court Chief Justice Robert French wrote the reasons for the decision were based upon constitutional provisions for executive power and did "not involve any judgment about the merits of public funding of chaplaincy services in schools".



The ruling relates to a case brought by Queensland father Ronald Williams and was heard by the full bench of the court in August 2011.



Mr Williams had four children attending Darling Heights State School in Toowoomba, west of Brisbane, where there has been a chaplain funded under the national program since 2007.



As well as arguing payments for the program were invalid, he also challenged it on the grounds of the Constitution banning religious tests for Commonwealth officers.



The court unanimously dismissed that part of the challenge, saying chaplains employed by SUQ did not hold office under the Commonwealth.

Originally published as Landmark ruling affects chaplains only - Roxon