A senior Victorian public servant "shaken to the core" by the horrific sexual abuse of children in state-run youth centres has admitted the problem is not limited to the past.
Department of Health and Human Services secretary Dr Pradeep Philip says there is no one who would not be deeply shocked, saddened and appalled by what some children in state care lived through.
"These experiences are abhorrent and should never have occurred," Dr Philip told the child abuse royal commission on Friday.
"As a father, I am shaken to the core that children and young people were forced to endure such horrific experiences.
"As a public servant, I am profoundly disappointed in the failures of our public institutions that led to or compounded the tragedies that have emerged through these hearings."
The commission's public hearing has focused on abuse in three state-run facilities from the 1960s to the '90s, but Dr Philip admitted this was not just a historical problem.
He told the commission there were 121 reports of incidents involving sexual behaviour in Victoria's juvenile justice system between January 2005 and June 2015.
Sixteen of these incidents were classed as falling in the highest category of sexual assaults, and Dr Philip said there had already been two reports of sexual abuse in 2015.
"So the fact that you have any is a concern. But this is a highly charged environment with a cohort where this is a real issue," he said.
Dr Philip said the youth system is very different today, with wards of the state dealt with separately from juvenile offenders. In the past, the two groups were put in the same institutions.
Victoria has the lowest rate of children in youth justice detention in Australia, Dr Philip said, as the state tries to allow more offenders to serve time in community-based services rather than in its two youth justice centres.
He said there has been significant changes to facilities and departmental practices, including in terms of the staff it employs, since a 2010 ombudsman's report identified systemic failures in these centres.
The Turana, Winlaton and Baltara youth training centres at the centre of the commission's hearing closed in the early 1990s.
Dr Philip said the department could and should have done more to protect children from harm caused by unacceptable practices and failings while they were under the care of the state.
"I offer my sincere and unreserved apology to all who have been affected by these failures and unacceptable practices," he said.
He extended the apology to those people abused in other state-run facilities.
Care Leavers Australia Network executive officer Leonie Sheedy said the apology should go to the families of children in state care as well.
"I don't think the department really cares what happened to us," Ms Sheedy said after the two-week hearing ended.
"We were Victoria's throw-away children."
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