A number of detainees breached their cells about 8.30pm on Tuesday and gained access to the grounds of the facility before climbing onto the roof.
They lit fires in several accommodation blocks and caused extensive damage, authorities said.
Corrective Services Special Operations Group were being supported by a large police contingent - including the Regional Operations Group Polair and the K9 Unit - in trying to contain the incident, a Department of Justice spokeswoman said on Wednesday morning.
"Some of the detainees on the centre's roof structures have begun surrendering to staff but the incident is still ongoing," she said.
"The Department of Fire and Emergency Services has extinguished the fires and is continuing to monitor the infrastructure."
The department earlier said attempts to negotiate with the detainees were continuing and a number remained on the roof, throwing projectiles.
Others were trying to obstruct access to firefighters working to extinguish the blazes.
Significant damage was caused across the site over several hours although there have been no reported injuries.
The Department of Justice said about 47 detainees were involved in the violence with others moved to a secure area, remaining under staff supervision.
There is no threat to the broader community.
Banksia Hill is a juvenile facility for offenders aged 10 to 17.
A guard suffered a suspected fractured skull after being hit by objects allegedly thrown by detainees at Banksia Hill in February.
Seven climbed fences and rooftops after absconding from activities outside their cells, and allegedly ripped pieces of masonry and metal off the facilities and threw them at youth custodial officers, four of whom were injured.
The union for Banksia Hill's youth custodial officers said it has significant concerns for its members at the centre.
The CPSU/CSA also said it was working with the justice department to ensure a safe end to the incident.
"We are encouraged to hear there have not been any injuries to staff or detained young people," a spokesman said.