One man is continuing his fight to end Commonwealth funding of chaplaincy in schools.

The High Court ruled that Federal funding schemes for the National School Chaplaincy and Student Welfare program were invalid after a challenge by Ron Williams, whose children attend Queensland public schools.

The Rudd government had moved quickly to pass a new law that would maintain the program and more than 400 others potentially affected by the ruling.

Now, Mr Williams has launched another challenge in the High Court to attack the validity of that law, and he has the backing of state governments.

State education authorities are concerned about the Federal Government undermining them by forcing the religious representatives into schools.

“We're back because they enacted legislation that even George Brandis, as shadow attorney-general ... said was inadequate,” Mr Williams told the ABC.

“He's quoted in Hansard saying that the government was looking for another clobbering in the High Court. Now here we are.

“This is simply about seeing that the Commonwealth doesn't keep funding such exercises. It got completely out of hand and has now cost nearly half a billion dollars.”

A key point in the case questions whether the executive government should be allowed to fund such programs, subverting state governments and going through local organisations.

Now in its final day, the new trial and the validity of the program has come down to a single word - whether the Commonwealth can prove school chaplaincy is measurably
“beneficial” to students.

“It has got down to the 'benefit for students', which is like trying to define a rainbow,” Mr Williams told the Toowoomba Chronicle.

“It is kind of new territory for the Commonwealth.

“They normally have programs where, at the end of it all, there has to be an outcome... if they are funding for a new highway or bridge to be built, in the national interest, there has to be an outcome - that bridge has to be built.”

“But how to define what ‘benefit’ is ... no-one can really say.”

The program was introduced by the Howard government, and originally awarded each school up to $20,000 each.

Mr Williams says the program has snowballed into an abominable taxpayer cost.

“It had very humble beginnings,” Mr Williams said.

“It was a man in Mount Martha who was an Access Ministries religious instruction volunteer who had an idea and took it to Greg Hunt, who took it to John Howard, and here we are - it's become a half-billion-dollar behemoth.”

Scripture Union Queensland is a Christian not-for-profit group which has advocated for the agreement with the Commonwealth.

Chief executive Peter James wants the law to stay.

“School chaplaincy is a tool that helps students thrive and achieve their educational potential,” he said told reporters this week.

“The court heard how students benefit from chaplaincy in helping them deal with emotional and social needs [and] that our national parliament has decided that school chaplaincy is an important part of the spectrum of educational support.”