The chief executive of the royal commission into child sexual abuse has resigned.

Janette Dines was appointed to the commission in late 2012 and was previously the director-general of Emergency Management Australia.

Ms Dines, who has been a Commonwealth public servant for 20 years, will leave the position on June 6.

While the circumstances surrounding her departure remain unclear, the ABC understands Ms Dines will be returning to a previous role.

The Royal Commission into Institutional Responses to Child Sexual Abuse began hearing evidence from victims of child sexual abuse early last year and has heard from more than 1,500 witnesses, with more than 150 cases of abuse being referred to police for investigation.

The royal commission, led by Justice Peter McClellan, is due to hold two days of private sessions in Adelaide starting on Thursday.

Justice McClellan said Ms Dines has been the driving force behind the establishment of the office of the royal commission since its announcement in late 2012.

"Ms Dines has successfully created the structure and facilities that have enabled the royal commission to achieve a large amount in a short time," he said in a statement.

But support groups for victims are worried that the resignation has come at a pivotal point for the royal commission.

Hetty Johnston from Bravehearts says Ms Dines was committed to the position and her resignation came as a shock to many.

"I'm filled with trepidation ... I'm frightened, I'm sad and I'm scared," she said.

"She's the glue, if you like, that makes this happen and sticks it all together.

"When you've got Janette resigning, you can't help but have a level of trepidation about where this is all going."

Craig Hughes-Cashmore from the Survivors and Mates Support Network says Ms Dines "really understood the issues".

"We're a relatively new charity and we had met with Janette a number of times since the very inception of the royal commission and she's been really supportive," he said.

Ms Dines said she was pleased to leave the commission in good shape to meet the challenges ahead.

Calls for certainty on the future of the royal commission

In April, Justice McClellan said that more than 40 people a week were approaching the commission to give evidence and that the commission did not have the resources to listen to all of them.

Dr Cathy Kezelman from Adults Surviving Child Abuse says the commission has already "done an enormous amount of work" but says the shock resignation highlights her broader concerns about the future of the royal commission.

"It's (the royal commission) set to continue to the end of 2015, but we also know there's been a request for a two-year extension," she said.

"The commission's made important inroads and it would be a great pity to see it terminated too soon.

"It'd be nice to hear from the Attorney-General that we can have surety that this ... is going to continue."

But Francis Sullivan from the Catholic Church's Truth, Justice and Healing Council says the commission is as strong as ever.

"I've very confident the royal commission has a future for as long as it needs it," he said.

"This Government, like the previous government, recognises that there's a social issue at stake here.

"We as a community should be thankful that people are prepared to put their hands up and do this task. It's gruelling, it's necessary, and, as a moment in Australia's history, it's extraordinarily important."

News of Ms Dines' resignation comes as The Christian Brothers today announced that they are re-examining a number of settlements with victims with some taking up the offer of ongoing counselling.

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