CANBERRA, May 8 - The Federal Budget includes nearly $250 million over four years to cement the at-times controversial pastoral care program in Australian schools.

"We are extending the national schools chaplaincy program on a permanent basis with a special new anti-bullying focus", the 2018/19 Budget papers state.

Many Coalition MPs and others opposed the secular "safe schools" anti-bullying program because they thought it went too far in terms of discussing gender and sexuality issues.

The money hasn't received a warm welcome from some in the education sector.

The Australian Education Union national president Correna Haythorpe said the budget didn't prioritise children and that chaplain funds could be better spent elsewhere.

"These funds are desperately needed in our schools to provide professional schoolcounselling services, ongoing professional development for principals and teachers and student wellbeing programs," she said.