Labor says a WA Government decision to cut chaplaincy funding to more than 100 public schools weeks before Christmas is a "disgrace".

Education Minister Peter Collier has blamed the Federal Government for a loss of funding.

The Education Department announced this week the number of public schools to receive the chaplaincy funding would be cut from 357 to 247.

However, 60 Catholic schools and 54 independent schools will receive money for chaplains in 2015 and 2016, an increase of 25 schools for those sectors on this year.

Opposition education spokeswoman Sue Ellery said the State Government chose not to fill the funding gap or argue the case with the Abbot Government.

Ms Ellery said it was "disgrace" schools learned they suddenly had no chaplains just before Christmas.

"[Mr Collier's] chosen to tell them just before Christmas," she said.

"He's chosen not to top up the funds. He's made his decisions that WA schools are going to be caught on the hop trying to re-adjust to a cut from his mate Tony Abbott."

Federal funding for public school chaplains over

But Mr Collier said a previous federally-funded chaplaincy program for 357 WA public schools had ended.

It came after the High Court ruled in June it was constitutionally invalid for the Federal Goverment to directly fund chaplaincy organisations.

"A new offer was made by the Commonwealth, which decreased the money available," Mr Collier said.

Under the terms of the State Government's new agreement with Canberra, a panel decided which schools would be funded.

Schools were assessed on location, student numbers, percentage of regular attendees, the current pastoral care support available, and socio-economic disadvantage.

Ms Ellery said the funding model was fundamentally flawed.

"It took no account of the fact that 87 per cent of children in Western Australia who come from low socio-economic backgrounds and who have complex family issues are in the public sector," she said.

Schools to raise own funds for chaplains

Balcatta Senior High School P&C President Helen Notis said her school would struggle to raise its own funds for a chaplain now that its funding had been cut.

She said chaplains were important because they were someone children could confide in about their problems.

"We have a need for a chaplain, our schools has a need for a chaplain, our community has a need for a chaplain and we will be doing what we can to retain a chaplain in our school," Ms Notis.

Warwick Senior High School chaplain Troy Anderson said his school would raise funds to keep him on.

"I was shocked and really disappointed, and not just for me but for our children," he said.

"I think there's so much need in my school that I've seen myself working there.

"For our children to lose that support, for the families and our community and the teachers to lose that support, I was worried and disappointed they'd have nowhere else to turn to."