Police fired tear gas and water cannon to disperse rock-throwing supporters of the white-bearded 65-year-old cleric shortly before his release from a Jakarta prison at around 7:00 am (0000 GMT) on Friday.
Seconds after he stepped out of Salemba jail after serving a sentence for immigration offences, a detective showed Bashir a warrant for his arrest under an "anti-terror" law which allows six months' detention without trial.
"Yes, sir," Bashir replied. "There is no problem."
"God's will must be accepted," he told reporters on arrival at national police headquarters in an armoured vehicle.
An appeal court overturned Bashir's 2003 conviction for involvement with the Jemaah Islamiyah, which they allege has links with al-Qaida. But police say they have new evidence that he led the group.
Bashir supporters accuse Jakarta
of bowing to US pressure
"We will challenge this in court. This is not an arrest, this is kidnapping," said one of Bashir's lawyers, Ahmad Khalid, outside the jail.
Ansyaad Mbai, who heads the security ministry's "anti-terrorism" desk, said the charges will relate 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 Bakr Bashir is the leader of JI."
Some 600 police in riot gear arrived before dawn outside the prison. At first they tried to negotiate with an estimated 700 furious supporters shouting "Allahu Akbar!" (God is greatest).
Then water cannon began spraying the crowd, who responded with a hail of rocks and bottles. Police picked up some rocks and tossed them back.
"We will challenge this in court. This is not an arrest, this is kidnapping"
Ahmad Khalid, Bashir's lawyer
Islamic groups as well as Bashir himself accuse Jakarta of bowing to US pressure.
National police spokesman Paiman denied this and said it was "not a problem" if Bashir refuses to talk. "There is other evidence material for a criminal case."
The US and other foreign governments insist Bashir led JI but prosecutors failed to convict him.
Last September a court jailed Bashir for four years for taking part in a JI plot to overthrow the government but said there was no proof he was the leader.
An appeal court in November overturned the treason conviction but ruled that Bashir must serve three years for immigration-related offences.
Last month the Supreme Court halved that sentence and said time spent in detention counted towards it - prompting expressions of dismay from the US, Australia and Singapore.