A damning report from Victoria's children's commissioner found that youth inmates have been subjected to "unacceptable" levels of isolation because of problems with staffing numbers and training.

In one shocking finding the report revealed some children and young people had been "completely isolated from their peers and routine of the centre" for 45 days.

The report found that four young people were isolated more than 100 times.

However, most instances of isolation were much shorter, with 23 per cent of recorded isolations for an hour.

The report comes after riots plaguing Victoria's overburdened youth detention centres.

Earlier this year, a group of inmates from the Malmsbury centre broke free and committed a series of serious crimes across the state.

At the Malmsbury centre, aggressive behaviour was the reason for almost 45 per cent of isolations, compared to almost 31 per cent at Parkville.

Commissioner for Children and Young People Liana Buchanan said her inquiry suggested isolation had been used to manage behaviour, rather than as a last resort, for short periods of time.

"This practice fails to recognise that isolation can cause severe short and long term harm to children and is simply not an effective way to address behavioural problems," she said.

The report revealed that whole units or entire centres were placed in lockdown at least 520 times over 18 months. Fifty of the lockdowns lasted more than 36 hours.

Ms Buchanan also slammed record keeping practices by the Department of Health and Human Services.

She has recommended "urgent measures" to improve compliance procedures for recording periods of isolation. She also called for immediate upgrades to youth justice isolation spaces to include sanitation, including toilets.

Some of the inmates were placed on so-called separation plans because they had been victims of assault or had attempted to take their own lives.

Youth Affairs Minister Jenny Mikakos said there was no doubt the report provided examples of longstanding and poor practice by the department.

She said the government "accepts or accepts in principle" all 21 recommendations made by the commissioner.

"The report shows the common reasons it is used include physical assaults, aggressive behaviour altercations, verbal abuse and attempted escape," she said."Isolation is used to de-escalate heightened behaviour and prevent a young person harming themselves, others or the facility."

Ms Mikakos said that, in the vast majority of cases, youth inmates were placed in lockdown in their own cells with access to "sanitation facilities".

The government has also committed to building a new high-security youth detention centre in Melbourne's outer west.

Community and Public Sector Union Victoria, secretary Karen Batt said it was well known the system had been in crisis for many years but it had been a "chicken and egg" problem.

"Assaults and violence inside lead to staff shortages which has been the contributing factor for extended lockdowns because otherwise clients would kill each other if left to mix without adequate staff," she said.

Opposition spokeswoman for children Georgie Crozier said the youth justice system was in chaos and dysfunction.

Commissioner for Aboriginal Children and Young People Andrew Jackomos said he was appalled by the high rates of Koori children being subjected to isolation.