Inmates in Victoria's troubled youth justice system have been confined to their rooms for weeks at a time, with others forced to relieve themselves on the floor of isolation rooms due to a lack of toilet facilities, the Commission for Children and Young People has found.

Key points: Inmates isolated for between 45-20 days during 18-month period of 'systematic over-reliance' on the practice

Inmates isolated for between 45-20 days during 18-month period of 'systematic over-reliance' on the practice In most cases youths were isolated in rooms, but in 1,700 cases they were sent to special isolation rooms

In most cases youths were isolated in rooms, but in 1,700 cases they were sent to special isolation rooms Minister accepts 21 recommendations but said the use of isolation was sometimes necessary

A report tabled in State Parliament found a "systematic over-reliance on isolation", which was imposed without appropriate authorisation during an 18-month period between February 2015 and July 2016.

The commission found cases of inmates isolated in their cells for 45 days, 31 days and 20 days for reasons including "threatened assault to staff" and "aggressive behaviour altercation".

The act governing the use of isolation, which involves locking young people away from other inmates and their normal routine, says the practice should be used in limited circumstances and not as a punishment.

The report said in more than 60 per cent of cases, inmates were isolated in their bedrooms, but over 1,700 cases of the practice involved the use of special isolation rooms.

"The lack of sanitation in some isolation rooms led to young people urinating, and at times defecating in isolation rooms," the report said.

"We also heard of children and young people in isolation rooms who were not given assistance when they requested it, and saw evidence of children being ignored during periods of self-harm."

The commission said it had trouble determining the scale of the problems because of poor or absent record keeping.

Isolation 'contrary to royal commission findings'

Commissioner for Children and Young People Liana Buchanan said isolation rooms could make the behaviour of young inmates worse.

Findings: There were 4,829 isolations recorded between February 2015 and July 2016

There were 4,829 isolations recorded between February 2015 and July 2016 Twenty-eight per cent of affected inmates experienced 25 or more isolations

Twenty-eight per cent of affected inmates experienced 25 or more isolations Figures likely "significantly underrepresent the total use of isolation" due to poor record-keeping

Figures likely "significantly underrepresent the total use of isolation" due to poor record-keeping The average number of daily isolations jumped dramatically from 8.8 to 42.4 following a riot at Parkville in November 2016

The average number of daily isolations jumped dramatically from 8.8 to 42.4 following a riot at Parkville in November 2016 The most common period of time in isolation was one hour

The most common period of time in isolation was one hour There were more than 20 isolations which lasted at least 24 hours

"They may calm down in the very short term but the fact that they're closed in to this very stark bare space for a long period starts to aggravate them again," she said.

"The act is very clear that isolation is not to be used as a form of punishment in our youth justice centres.

"The kids we spoke to were really clear that they think it is."

Commissioner for Aboriginal Children and Young People Andrew Jackomos said he was appalled by the high number of young Aboriginal people being isolated from other inmates.

"More than two thirds of isolations imposed on Koori kids were not appropriately authorised and cultural support workers are not being engaged as policy requires," Mr Jackomos said.

"Isolation as is being practised currently is contrary to the findings and principles of the Royal Commission into Aboriginal Deaths in Custody."

Families and Children Minister Jenny Mikakos said the Government accepted the report's 21 recommendations, including changing the Children, Youth and Families Act to provide further clarity around the use of isolation.

But she added the practice of isolation was sometimes necessary.

"We need to improve the capacity of our staff to de-escalate behaviour without needing to resort to these practices and this is why we are also rolling out improved staff training," she said.

"So there are a number of things already underway."