Seven men are being transferred from detention on Christmas Island to a West Australian prison, with restraints used to secure the "extreme risk individuals" during the charter flight.
The men were among a group who allegedly took part the "disturbance" at the centre, a spokeswoman for Immigration Minister Peter Dutton says.
Riot police had to use tear gas to quell the uprising on Tuesday, which was triggered by the death of detainee Fazel Chegeni Najad, an Iranian Kurdish refugee whose body was found outside the centre after he escaped on Sunday.
The Department of Immigration and Border Protection said the remaining detainees at the centre were being returned to accommodation compounds, which were being repaired as a priority.
It said they stayed overnight in "temporary but secure parts of the centre" and reports of detainees sleeping in cages were false.
Mr Dutton said the rioters caused more than $1 million worth of damage to the centre and the perpetrators would be prosecuted.
