Some survivors of abuse in state care are calling for the Government to separate the strands of its Royal Commission of Inquiry into Historical Abuse.
The Inquiry was announced more than a year ago, but late last year the Government bowed to pressure and included victims of abuse in faith-based institutions.
Since then, several Commissioners have faced conflict of interest allegations over their religious views, including Chair Sir Anand Satyanand, who is Catholic.
State care survivors Toni Jarvis and Kath Coster are now calling for the Government to hold two separate inquiries - one for victims of state abuse and the other for abuse in faith-based institutions - to prevent further issues from arising.
"They are two different institutions, run on different ideology of course, and they have different dynamics and ramifications. They could be seen as undermining or overshadowing each other," said Toni Jarvis.
"You add the word faith to it, you bring God into the picture - and when you bring God into the picture it's a completely different dynamic," Ms Coster said.
She's concerned the recent controversy could discourage victims from giving evidence.
"If you hear distrust, people get affected by that," she said. "It's going to make a difference to how much truth and how many stories come forward."
Inquiry leaders say they do not believe the faith of Commissioners will impact the inquiry and that they will soon publish all conflicts of interest.
"Unless the Inquiry also covered faith-based institutions, it is the Royal Commission's view there would have been an element of incompleteness and injustice," they said in a statement.
A spokesman for The Network for Survivors of Abuse in Faith-based Institutions said the organisation's main concern is the welfare of all survivors, but it wasn't keen to comment on the concerns raised before seeing more details of the Royal Commission's plans.
Internal Affairs Minister Tracey Martin told 1 NEWS that "extending the scope of the Inquiry was one of the most strongly argued issues during consultation", and that the Inquiry will have two separate reports to deal with state care and the abuse of children in faith-based institutions.
Private hearings will start in mid-2019, allowing everyone to have their say.