Federal and Northern Territory police are investigating the cause of a riot at the Darwin detention centre on Sunday.
The ABC reports order has been restored. Up to 100 people were involved in the riot.
The Immigration Department says the protest began when two men climbed a tree and refused to come down, and escalated to involve the majority of the Indonesian crew members detained in the centre. They are accused of people smuggling.
At first the department told the ABC the men were protesting over delays to their criminal cases, but later refused to speculate about the nature of their grievances.
As the riot unfolded, a large fire was lit outside and about a dozen men climbed onto the roof and were seen bashing it with long poles.
Federal police may lay charges for assault and affray as well as property damage.
The Immigration Department says a guard was treated at the scene for minor injuries.