Community leaders have vowed to find an alternate funding avenue to continue the chaplaincy program in Queensland schools.

Today's High Court ruling found Federal funding of chaplaincy programs in Queensland schools was unconstitutional, and the decision will impact around 2500 schools across Australia.

Scripture Union QLD incoming CEO Peter James said he would work closely with the Federal Government to devise a new funding model to continue chaplaincy.

Moreton Bay Regional Council mayor Allan Sutherland said he was "absolutely shattered" and council would continue to host chaplaincy breakfasts to support the program.

"There will be plenty of kids who will fall through the cracks if this isn't turned around," he said.

Patricks Road State School chaplain Andrea Eadie said students would be at a disadvantage without the services of a chaplain.

She said she still hoped the Federal Government would be able to find an alternate funding solution but said the school community was very supportive of the chaplaincy program and would work to ensure the program's longevity.

Ms Eadie said chaplains provided "emotional first aid" and provided support to students coping with personal circumstances, like a family breakdown.

"You take out the chaplaincy role and the support that child needs on the day simply isn't there."

Reverend Alan Robinson, who chairs the Beenleigh region School Chaplaincy Support Committee, said nine schools in the area had opted to hire chaplains over other supportive staffing roles.

He said a fundraising dinner last month raised $20,000 to support school chaplains, indicating they were valued by the community.

Premier Campbell Newman said he was keen to work with the Federal Government to keep chaplains in schools.

Member for Everton and former Scripture Union Queensland CEO Tim Mander said: "The ruling suggests that funding could be provided through state grants. I strongly urge the federal government to follow this course."

"We cannot afford this potential loss for our youth and the community at large," Mr Mander said.