Security forces began evacuating the Kerobokan jail in Bali on Thursday after days of unrest during which inmates were able to seize control of the prison for a second time.
Troops stormed the prison at dawn on Wednesday to wrest control after a night of arson and stone-throwing, only to lose it again late that night.
All foreign and female inmates were being removed from the jail amid fears for their safety. Juvenile prisoners were also being evacuated.
The provincial military command says foreign and female prisoners are being removed amid fears they could be taken hostage.
The ABC reports the overcrowded prison was the scene of a riot last weekend, sparked by an internal feud that fed into prisoner grievances about the way Kerobokan was run.
Bali Nine member Scott Rush was the first Australian to be moved out of the prison.
But some other Australians, including Schapelle Corby and other members of the Bali Nine, said they wanted to stay.
The ABC reports the prison has more than 1015 inmates - more than three times its intended capacity.