Government documents detail the list of Canberra schools with student welfare workers, a workforce which the Abbott government did not want to fund as it favoured giving money toward religious chaplains.

While the Abbott government is pushing ahead with a religious-only school chaplaincy scheme, the ACT government says it will not administer it unless schools can choose secular counsellors.

ACT Education Minister Joy Burch said the territory was willing to negotiate with the Commonwealth and welcomed any additional funding for schools.

The government was forced to redesign its $244 million scheme after the High Court ruled it invalid in June and in a bid to prevent another legal challenge, the federal government will provide funding to state and territory governments to administer the scheme.

"There are 25 qualified welfare officers in Canberra who are going to pay the price for the Abbott government's ideological changes," Labor Senator Kate Lundy said.

"These are qualified individuals who have already worked hard to build trusting relationships within their school communities.

"Now those same welfare officers are facing the prospect of unemployment, merely because they do not have formal links to a religious institution.

"It is completely unacceptable that the Abbott government would try to force its own ideology onto our schools by disempowering local communities and putting the support for students at risk."

ACT Education Minister Joy Burch said the territory government would not administer the scheme unless schools could choose secular counsellors.

Liberal Senator Zed Seselja said the school chaplaincy program had been a great success and that Ms Burch's refusal to accept chaplaincy funding would put Canberra school children at a disadvantage.

Executive director of Blue Gum Community School Maureen Hartung said the $20,000 annual funding for the student welfare officer at her school would run out at the end of the year.

The money pays for 10 hours a week for someone to help give the students resilience skills, such as ways to deal with stress.

"This is the closest we have to a school counsellor," she said.

The 25 Canberra schools with student welfare workers were:

• Blue Gum Community School
• Bonython Primary
• Calwell High School
• Charles Conder Primary
• Charnwood-Dunlop School
• Cranleigh School
• Dickson College
• Emmaus Christian School
• Farrer Primary
• Gold Creek School
• Good Shepherd Primary School
• Gungahlin College
• Holy Spirit Catholic Primary School
• Kaleen Primary
• Kingsford Smith School
• Lanyon High
• Latham Primary
• Narrabundah College
• Sacred Heart Primary School
• St Francis Xavier College
• St John the Apostle Primary School
• St Monica's Primary School
• St Thomas Aquinas Primary School
• St Thomas Mores Primary School
• St Thomas the Apostle Primary School