The facilities have been under the spotlight in recent weeks following reports that up to a dozen mothers had attempted suicide at a detention centre on Christmas Island, an Australian territory in the Indian Ocean.
The women did so under the belief that their babies would have a better chance of being settled in Australia if they were orphans, reports said.
A leading psychiatrist alleged at a national inquiry into the mandatory detention of children seeking asylum that figures showing the extent of mental health issues had been covered up by the immigration department.
"(The Immigration Department) reacted with alarm and have asked us to withdraw these figures from our reporting," Young said.
Also Read
Immigration Department Secretary Martin Bowles told the inquiry: "If our staff did an inappropriate thing, then I will deal with that," the Australian Broadcasting Corporation reported.
Australian Human Rights Commissioner Gillian Triggs visited the Christmas Island centre this month and said many of the 174 children being held were plagued by despair and suffering symptoms consistent with post-traumatic stress disorder.
"If the information is being redacted, altered, before it gets to the minister then that is extremely concerning," she said on the sidelines of the inquiry.
"The minister has a responsibility to be much more transparent about what is happening.
"Where this is smothered in secrecy you get these kinds of processes where data is interfered with, statistics are changed or reporting is not given."
Morrison had yesterday called Triggs' claims that children in detention were self-harming, biting themselves, banging into furniture, and swallowing poisons "quite sensational".
Any boat people who arrived in Australia after July 19, 2013 cannot be resettled in the country, regardless of whether they are eventually judged to be genuine refugees. They are instead sent to camps in the Pacific for processing or resettlement.