High levels of staff absenteeism in the secure area of the Malmsbury Youth Justice Centre are putting employees at risk, the union says.
Julian Kennelly from the Community and Public Sector Union told the Bendigo Advertiser staff faced verbal and physical abuse, being spat on, and receiving threats of sexual assault.
Absenteeism rose when the institution was full or the mix of inmates was inappropriate, he said, which left those staff members at work more vulnerable.
Mr Kennelly said fewer staff also meant inmates in the secure area had to be rotated in and out of their cells to ensure they were appropriately supervised and this only added to the pressure of the situation.
Mr Kennelly said there was an "increased awareness of unrest" over recent months.
On Boxing Day last year, a staff member was taken to hospital after being injured and the month before a worker was hospitalised after being attacked.
Mr Kennelly said the staffing issue did not lie with the level of funding for employees, but how to fill the gaps when people did not go to work.
The system had not recovered since staff were "deprofessionalised" with cuts in 2011, he said, which led to fewer experienced youth justice workers.
This meant more short-fill agency staff were used, he said, but they were less likely to return to the centre if subject to a negative experience.
But Mr Kennelly said there had been an increase in the recruitment of permanent staff.
The Department of Justice and Community Safety did not respond to questions about the existence of the issue.
But a spokesperson said "considerable work" was done to improve safety and security, including the employment of more staff and security upgrades.
"More than 80 new staff have started work at the Malmsbury Youth Justice Precinct in the past 12 months, with the next new squad of up to 25 staff expected to be on the ground by late June," the spokesperson said.
"In recognition of the complexity and challenges of the role, the Department of Justice and Community Safety has established a dedicated health and wellbeing team and program to support Youth Justice staff."
A WorkSafe spokesman told the Bendigo Advertiser the watchdog was aware of concerns and was making inquiries.
Mr Kennelly said the capacity of Victoria's youth justice centres needed to improve, as did the management of more difficult inmates.
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