The Indonesian boat crew, who are facing people smuggling charges, set mattresses on fire and brandished poles on a roof at the centre on Sunday.
On Monday, 117 detainees continued the protest, with police called in to negotiate with the group, some of whom had climbed back onto the roof.
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Immigration department spokesman Sandi Logan said the situation had eased overnight and the centre was calm on Tuesday.
"All the protesters have come down off the roof and are in a secure area within the facility," he told AAP.
"Police remain on site. The protesters agreed to negotiate with police and detention centre staff and were escorted to a secure area within the facility.
"They were offered food and water."
Australian Federal Police are yet to say if they will charge the protesters.
The detention centre at the Coonawarra Naval Base currently houses 487 detainees, including 151 alleged Indonesian people smugglers.
