Accused Indonesian people smugglers set mattresses on fire and brandished poles on a roof during a protest that began around four o'clock yesterday morning (CST).
Department of Immigration spokesman Sandi Logan said the protesters were all Indonesian crewmen facing people-smuggling charges, but it's not clear what triggered the riot.
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Mr Logan says the next step will be to study CCTV vision, take statements from those who witnessed what occurred, and for the NT police to determine whether charges will be laid.
Authorities have said the protest started when two Indonesian crewmen climbed a tree and refused to come down.
Other detainees joined in, yelling and starting a fire in the yard by setting alight mattresses and paper about 7.30am.
Firefighters extinguished the fire, which caused a huge plume of black smoke to rise above Darwin's outskirts, by 8am.
Department of Immigration spokesman Sandi Logan said the protesters were all Indonesian crewmen facing people-smuggling charges, but it was not clear what had triggered the riot.
"Some of the protesters had gathered together refuse, paper and a couple of mattresses and thrown them into a pile out in the open compound area and lit that," he told Sky News.
"(The smoke) looked quite spectacular, but in fact, it has caused no building or structural damage.
"These sorts of actions will not benefit the detainees inside the detention centre."
Some protesters climbed on to a rooftop and brandished poles during the protest but they had returned to their rooms, Mr Logan said.
The detention centre at the Coonawarra naval base houses 500 detainees, including 150 alleged Indonesian people smugglers.
Immigration department officials cannot confirm how many detainees were involved in the protest but believe it could be up to 97 - the total number of Indonesian crewman detained in the compound.
Jack Smit of human rights group Project SafeCom says the incident can be easily explained by the government's inhumane treatment of people in detention centres.
"If you take the open communication with the world away from people in long-term detention, if you store them in overcrowded facilities, if you lock them up without progressing their case assessment, then you dehumanise them," he said.
"You create the same monster as former immigration minister Philip Ruddock created during the days of John Howard."
NT police officers were at the centre, but the force declined to comment.
