Despite an extra $245 million in funding for the program, schools will have choices for chaplaincy reduced.

Schools will lose the option of appointing secular social workers under the national school chaplaincy program, for which the Abbott government has pledged funding over five years.

It is now religious chaplaincy or nothing, according to Education Minister Christopher Pyne, who says the $245 million fund is for “pastoral care” specifically.

This does not include ‘pastoral’ in the agricultural sense.

Pyne has confirmed cuts to the Labor government’s allowance for schools to bring in a non-religious student welfare worker as an alternative to a chaplain.

Like many of the most savage cuts in the latest budget, Mr Pyne says it is an issue for the states.

“Counsellors and social workers in schools are really the responsibility of the states and territories,” Pyne told Guardian reporters on Wednesday.

“So where does the Australian constitution say that the federal government is responsible for school chaplains?” replied Australian Education president Angelo Gavrielatos.

Figures show 3,527 schools have been receiving support of $20,000 a year to engage chaplaincy or student welfare services under the existing program.

The Education Department says 623 schools brought in a student welfare worker rather than a chaplain.

The new budget papers say number of schools to be supported will drop to 2,900 under the new scheme.

The budget papers indicate “simplified reporting and administrative requirements [will] allow funding recipients to better focus on delivering chaplain services”.

Parliamentary secretary for education, Senator Scott Ryan said the Federal Government wanted specifically to restore the original Howard government vision for the program, which did not include secular assistance.