The Department of Education has conceded a number of students in south coast schools have no choice but to sit in scripture classes, despite their objections.

Due to a shortage of teachers and class rooms, some students at Nowra and Ulladulla public high schools have to sit at the back of the scripture class.

They are told to participate in quiet activities, but are not allowed to read a book or listen to music with headphones.

Maria Grey-Spence, the South Coast regional director with the Education Department says she was told just yesterday about the arrangements.

"We are now working with those schools to ensure that the students will be separately supervised and accommodated in line with the policy," she said.

One parent told the ABC her daughter came home distressed after being told God is going to burn the world, while another parent says her child walked out of class when the religious instructor claimed he could 'cure' homosexuals.

A third parent Glen says children with non-christian faiths at Nowra High School are allowed go to the library during religious classes, but atheists are treated differently.

"At Nowra High School if you are a Muslim or a Hindu or something along those lines you can actually go to the library during scripture classes, but as an atheist he has to go to the same room as kids on detention, kids being punished are in," he said.