The federal and several state governments have stopped counting complaints against the school chaplains program and no states keep records of the faith of those providing pastoral care.

Since the federal government handed responsibility to the states for administering the program in 2015 after a high court challenge, several states including New South Wales, Queensland and Western Australia have not centrally recorded complaints against it.

The Turnbull government is expected to extend funding for the program in the 2018 budget, after a group of MPs including Luke Howarth lobbied for it, despite the fact the federal education department has lost oversight and does not record complaints against the program.

The program is controversial because in 2014 the Abbott government specified that chaplains could not be secular social workers and must be ordained religious people.

Although chaplains are not allowed to proselytise, nothing prevents them speaking about their faith and some religious organisations such as the Anglican church of Noosa openly acknowledge that chaplains refer students and their families to church.

Before 2015, complaints against the chaplains program were reported in Senate estimates, along with the breakdown of the faiths of the pastoral care workers. But the high court ruled in 2014 that the commonwealth could not fund the program directly, which meant the commonwealth instead provided grants to state and territory governments to administer it.

But after states gained responsibility in 2015, education departments adopted different approaches, with Victoria and the Australian Capital Territory recording complaints centrally and others imposing no such requirement on schools.

A spokesman for the NSW education department said the department encouraged parents and students to raise issues locally “where they can be resolved by someone who has sufficient knowledge and authority to decide what should happen as a result of the complaint”.

“Any records relating to these complaints are generally held locally and the department does not have a mechanism to report on the total number of complaints made in relation to the program in 2014, 2015, 2016 and 2017,” he said.

Western Australia and Queensland also do not centrally record complaints. A spokesman from the Queensland education department said complaints were “addressed with priority at the local level”.

A spokeswoman for the Tasmanian education department said its guidelines suggested parents and students raised complaints at the school level.

She said the department had received two complaints in 2016 but there was “no clear evidence of a breach of any agreement or guidelines” and no other complaints had been made since 2014.

Spokespeople for the education departments in South Australia, the Northern Territory and Australian Capital Territory said that no formal complaints had been recorded by the department against the chaplains program since 2014.

Federal education minister Simon Birmingham said that the high court had determined that state governments are responsible for running the chaplains program and states were “best placed to ensure it’s being delivered effectively in their jurisdiction”.

States and territories are not required to record the faiths of chaplains, and none were able to provide a breakdown.

In 2015 federal education department officials told Senate estimates that in the previous year, 2,312 of the program’s 2,336 chaplains were Christian. The rest were adherents of Islam (13), Judaism (8), and there was one each from Bahai, Buddhism and Aboriginal traditional religions.

A spokeswoman for the Western Australian education department said the program was voluntary and “the nature of chaplaincy services, where provided, is decided by each school and its community”.

In March a group of secular societies wrote to the Australian Human Rights Commission seeking a review of the chaplains program on the basis it may harm freedom of religion because non-religious people cannot be hired for the roles.

In a 2015 consultation report the commission reported that complaints had been raised about the chaplains program at almost all of its public meetings.

It said while the program varied between schools, many people raised the “implications of government paying religious organisations to provide chaplaincy services in public schools that would otherwise be provided free at a place of worship”.

The commission’s president, Rosalind Croucher, who is also sitting on Philip Ruddock’s religious freedom review panel, told Guardian Australia it did not propose to conduct an inquiry into the chaplains program.

“We are hopeful that the religious freedom review might be a catalyst for more discussion of the issue,” she said. “The commission exercises its inquiry function sparingly and within the limits of its available resources.”

Guardian Australia understands that Labor is likely to retain the chaplains program but return the ability to hire non-religious people to provide pastoral care, as was allowed under the last Labor government.