She has also hit back at Immigration Minister Scott Morrison, saying he needs to be better advised about what is happening inside Australia's detention centres.
Today's hearing into children in detention 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 this month.
He said IHMS had collected figures showing "significant" mental health problems among a significant number of child detainees.
Professor Triggs says 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," Professor Triggs told the ABC's 7:30 program.
"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."
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.
Professor Triggs has repeatedly warned of conditions inside the Christmas Island detention centre.
After visiting the centre in recent weeks, she declared that virtually all the 174 children there were sick and that conditions had worsened since earlier in the year.
Morrison 'needs to be better advised': Triggs
Last night, the Immigration Minister said Professor Triggs was not a doctor and described her claims of children attempting self-harm as "quite sensational".
"We have medical people who are there who provide that care on a daily basis," Mr Morrison said.
But Professor Triggs has suggested the Minister "needs to be better advised" about what is happening.
She says the evidence provided to the commission's year-long inquiry so far corroborates her statements as being accurate and that children are attempting self-harm.
"One of the examples was drinking detergents, the head-banging was very common, jumping off heights, we heard others of plastic bags over the head, using the hijab to hang," she said.
"There were children with big lumps, untreated sores, red eyes. But most of them were coughing, had asthmatic conditions or stomach complaints."
She said that if children in the community were treated that way, people would be demanding action.
Today'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.