Among the foreigners in the infamous prison are 12 Australians, including Schapelle Corby and the Bali Nine.

Several "tactical" vehicles have been moved close to the entrance of the jail, provincial military command spokesman Wing Handoko said.

They also plan to move about 120 women from the prison before they "clean it up".

Mr Handoko said they intended to evacuate the woman and foreign prisoners for their own safety.

He said authorities feared they would be taken hostage within the jail by "troublemakers".

Pressed on what would happen to the other 800 prisoners, Mr Handoko said that they would "clean it up", referring to the prison.

Earlier, prison and other sources have told Fairfax that the facility will be closed this afternoon and all 1015 prisoners moved out, including one police source that said the operation would begin 2pm (local time).

Senior police and military figures have been at the prison for much of the night after two nights of rioting that saw inmates seize control of the facility.

Earlier today, local time, a water cannon truck moved into the forecourt of the prison.

Army personnel amassed outside the walls of the desperately overcrowded prison at about 10am local time.

Sources have suggested that most of the prison's 1015 inmates will be moved by military aircraft to another location in Indonesia, understood to be Surabaya, on the island of Java.

Different scenarios were planned, including one that would leave more than 50 foreign prisoners in place at Kerobokan, including Australian drug traffickers Schapelle Corby and the Bali Nine.

However, it's understood the latest plan is to move all prisoners out of the fire-damaged prison, but to relocate the Australians and other "foreigners" to another location within Bali.

The administration building, governor's office and entrance of Kerobokan prison were entirely gutted in riots on Tuesday night and Wednesday morning, which caused authorities to evacuate the grounds and cede control to the inmates.

Three inmates were injured by rubber bullets as police reasserted control after daylight on Wednesday. The three were taken out of the prison for treatment and questioning.

A second riot last night involved inmates hurling rocks and flaming missiles over the walls and shouting for the return of the three injured who had been removed the previous night. Police once again evacuated the prison, and quelled the crowds by firing into the air.

The view into the prison this morning showed that a barbed wire fence had been pushed to the ground. Workers are trying to restore electricity and security to the prison, by nailing corrugated iron sheets over the gap left when windows were shattered by the fire.

However, Fairfax understands that authorities believe the prison is now no longer able to be secured. It is as yet unclear where they intend to rehouse the prisoners.Official confirmation has been sought but so far, a military spokesman has declined to comment.