The Immigration Department says the detainees protested about food and the fact the air conditioning was not working as a result of a power outage.
A group of about 10 detainees from another part of the centre jumped the fence to join the protest, bringing the overall number of those involved to 50.
The protest has now ended.
The search for survivors from Wednesday’s boat wreck continued today, but Prime Minister Julia Gillard says it is unlikely anyone else will be found alive.
There are 42 survivors from the incident, while at least 30 people have died.
Ms Gillard says it may never be known exactly how many people were on the boat.
She says a memorial service for those killed will be held in the next few days.