Parents have warned the secular public school system is under threat from the school chaplain program.
Parents & Citizens Council president Elizabeth Singer has received numerous complaints from parents that ''the lines are being blurred between religious and secular concerns''.
Ms Singer said schools were being forced to turn to school chaplains because of inadequate funding and teacher training for crucial development programs.
''Funding has not been available in another form that they [schools] could use so they have had to turn to chaplains. But the curriculum programs need to be designed to be delivered by appropriately trained teachers,'' she said.
''We have received complaints from families that schools are having to rely on chaplains to meet the social and emotional needs of the students. In government schools there is a feeling that this should be delivered by secularly trained people.''
But Ms Singer said there had been no complaints about controversial group Focus on the Family.
Education Minister Andrew Barr launched an investigation into Focus on the Family last week after allegations students in four schools Canberra High, Melrose High, Campbell High and Stromlo High may have attended drug and sex education seminars without parental permission.
A student at Canberra High School also alleged homosexuals had been denigrated during the sessions and inappropriate remarks about sex had been made.
Focus on the Family chief executive Brett McLeod has hit back at the ACT Government's investigation, saying he was disappointed the Government had not talked to his organisation before launching an investigation.
''How do the seminars run for two years without complaint? Surely something should have happened before now and on that basis an approach could have been made to us first I would have expected that,'' he said.
''We seek to fully cooperate with every aspect of that investigation and we actually welcome it ... if the allegations are true that would surprise me.''
Mr McLeod also defended Focus on the Family's views on homosexuality.
''Personally, and for the organisation, I do not see myself as having the right or the authority to make a judgment call on how someone conducts their life according to their belief system and I will never do that provided they are conducting their life within the law,'' he said.
The investigation into the religious group is expected to be completed in the next month.
The education department confirmed it had requested copies of the notes used in the ''No Apologies Impact seminar'' presented to Year 9 and 10 students in the ACT, but the department has not met either Mr McLeod or seminar presenter Marc Erbsleben. Mr Erbsleben refused to comment for this story.
Mr Barr defended the investigation.
''I take any allegation of inappropriate matters being taught in ACT public schools very seriously,'' he said. Some of the subject mattermight not have been appropriate for high school-aged students.