The Refugee Council is demanding Immigration Department staff be sacked if they were involved in a cover-up about the scale of mental health issues among child asylum seekers in detention.

Yesterday a Human Rights Commission inquiry was told that Immigration Department officials reacted with alarm at figures showing the extent of mental health concerns among young detainees.

"[They] asked us to withdraw these figures from our reporting," psychiatrist Dr Peter Young said.

Dr Young was the director of mental health services at detention centre service provider International Health and Mental Services (IHMS) for three years until earlier last month.

Paul Power from the Refugee Council says if the claims are true, the staff involved should be sacked.

"We can't have this culture of misleading the public in such a vital area of public policy," he said.

"It's not tenable for people to be holding senior positions within the Department of Immigration if what they're attempting to do is to hide the implications of their policies from the Australian public."

Immigration Department secretary Martin Bowles told the inquiry that he was not aware of any cover up, but added that if department staff had acted inappropriately, he would take action.

Mr Power says Immigration Minister Scott Morrison needs to set up a thorough investigation into the claims.

"The Government needs to be acting immediately. It can't wait for some months before the Human Rights Commission inquiry is concluded," he said.

"And also, unfortunately, successive governments – both Labor and Coalition – in the past have taken little notice of Human Rights Commission inquiries."

The president of the Human Rights Commission, Professor Gillian Triggs, last night described Dr Young's evidence as "very troubling and damning".

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 7 minutes 49 seconds 7 m Gillian Triggs speaks to 7.30's Sarah Ferguson

She told ABC's 7.30 program the data shows the incidence of mental health problems among children detainees is about 30 per cent higher than the normal child population.

"[Dr Young] gave evidence that he was asked to withdraw those figures and to resubmit them in some more palatable way," she said.

"That was very, very troubling and damning evidence. We're coming across what you'd see perhaps as a manipulation of the circumstances.

"There seems to be ... almost a systemic process within the [Immigration] Department to keep these figures under some sort of wrap – they're not being analysed, they're not being considered."

Mr Morrison has agreed to appear at the inquiry at a later date.

Thursday's inquiry hearing came the day after Australian church leaders accused the Federal Government of "state-sanctioned child abuse" over its treatment of unaccompanied asylum seeker children.