Paramilitary police in riot gear fired tear gas and water cannon to disperse hundreds of rock-throwing supporters outside Jakarta's Salemba jail before Bashir emerged after serving a sentence for immigration offences.

He was re-arrested under an anti-terror law, telling reporters after being taken to national police headquarters by armoured vehicle, "God's will must be accepted."

Police said Bashir, as alleged former leader of the Al-Qaeda-linked Jemaah Islamiyah (JI) network, would be charged with the Bali nightclub attacks which killed 202 people in October 2002. Most victims were young Western holidaymakers.

Asked what charges Bashir faced, national detective chief Suyatno Landung said: "Many cases from 1999 to 2002, (including) that one in Bali."

Ansyaad Mbai, who heads the security ministry's anti-terrorism desk, told AFP Bashir would face charges relating to "terrorism cases in Indonesia, starting in 2000 until the Bali bombing and the Marriott bombing."

"The culprits are JI and JI is led by him. That is the connection," Mbai said. "Now the police have proof that Abu Bakar Bashir is the leader of JI."