Dan Tehan responded to the move on Sunday, saying the ACT government should tell parents why their children wouldn't be supported by chaplains next year.

The ACT government has proposed keeping the chaplains in non-religious pastoral support roles after the federal government rejected a territory request to extend its national chaplaincy funding to secular welfare workers.

Deputy Chief Minister and territory Education Minister Yvette Berry defended her decision, saying most public school parents and teachers she had spoken to agreed chaplains were not consistent with the secular status of public schools.

Mr Tehan said more than 1000 schools had written to the federal government about the important role of chaplains.

"It's disappointing the ACT government will deny students access to these important services, that include anti-bullying support," he said.

Ms Berry said the government had told chaplains employed in ACT public schools and the Scripture Union, an affiliate of the group providing chaplaincy services, that following a transition this year, the workers could continue as direct government employees offering secular pastoral support.

"I recognise these people often have a valued place in school communities," she said.

The ACT government's decision to ban religiously-affiliated chaplaincy in public schools "should have no impact on non-government schools", Ms Berry said.

"Minister Tehan needs to explain why he sees religious affiliation as so integral to providing social and emotional support in government schools," she said.

Under the federal Labor policy on school chaplaincy, schools would decide whether to use funding for secular or religiously-affiliated staff. The Coalition government in May funded the program with $247 million over four years, but requires workers have a religious affiliation.

Ms Berry recently told Scripture Union the ACT government would end religiously-affiliated chaplaincy in government schools by the end of 2019.

She says the ACT Education Act required schools to operate in a secular, non-sectarian way and religious chaplains were incompatible with this objective.

School Chaplaincy ACT chief executive Peter James said Ms Berry was ignoring part of the legislation saying a high quality education recognised the religious needs of students.

The decision came as a surprise and chaplains wouldn't be able to assist students as well without offering spiritual support, he said.

"It's like trying to suggest the fruit will still be there when you kill the tree," Mr James said.

Chaplaincy had been popular in schools for 26 years, and had played a "non-coercive, non-manipulative" role.

"Chaplains are not telling students what to believe, but they are available to them," he said.