Public schools in the Northern Territory already provide value-building and there is no place for chaplains permanently on their grounds, the main body that represents families of those schools says.

President of the Australian Council of State School Organisations (ACSSO) Peter Garrigan told the ABC public schools risked becoming recruiting grounds for Christian groups under the federal government's plan.

"When you put those people into a school you can't expect them not to proselytise, because that is their background, and therefore they are going to want to convert," Mr Garrigan said.

He said NT government schools already had a very strong values based sytem with their students without chaplains and there was no place for religious figures permanently on their grounds.

"It would be my advice that the money should be spent elsewhere," he said.

Under plans outlined in the federal budget the government will spend $245m to be spent on chaplains in public schools, but funding under the program will no longer be allowed to be spent on secular counsellors or psychologists.

"The mix of students that you have got in the Territory, provides a wealth of value-building, acceptance, the building of community that happens when your child is attending such a multicultural classroom is beyond calculation," Mr Garrigan said.

"You can't look at it from a very focused Christian background when that is the role of the parent, or the parents, to ensure that their child gets the religious or moral upbringing that they want them to have, not the school or not the chaplaincy program as such," he said.

Mr Garrigan said nearly all chaplains in Australia were Christian, and he agreed with the concerns of a talkback caller who questioned how Muslim children who needed counselling would be able to seek help under the new plans.

Christian groups who had chaplains in schools in Victoria and Queensland have claimed strong success in gathering young children into the fold, he said.

Federal Education Minister Christopher Pyne has defended the decision to strip funding for counsellors and social workers from the school chaplaincy program, saying their inclusion was the responsibility of the states and territories.

A call to the Catholic Education Office in Darwin seeking information on whether they would be seek to install priests in public schools was not immediately returned.