Bashir was picked up by his family and was told to his home in Java, a spokesman, of the Directorate-General for Corrections at the Ministry of Justice and Human Rights.
Photos showed him wearing a white robe, white cap and a face mask as he left the Bogor prison in southern Jakarta.
“Abu Bakar Bashir was released from Gunung Sindur Prison at 05:30,” spokeswoman Rika Aprianti told reporters, adding that he was healthy with his departure.
Bashir, 82, who is considered the spiritual leader of Jemaah Islamiah (JI), a jihadist network linked to al-Qaeda, was jailed for 15 years in 2011 for links to a militant training camp in the Aceh. province.
After periodically reducing his prison sentence, he served ten years in prison.
Although Indonesian police and Western intelligence agencies say Bashir was linked to the attacks on Bali that killed 202 people and an attack on the JW Marriott Hotel in Jakarta in 2003, he was never convicted and he deny ties.
88 Australians were killed during the bombings in Bali, and the country’s foreign minister, Marise Payne, said this week that Indonesia should ensure that Bashir does not incite more violence.
Thiolina Marpaung, an Indonesian who was wounded during the attacks in 2002, said she wanted authorities to oversee Bashir.
“We do not know what he did in prison,” she said by telephone. “The government must continue to exercise control over the terrorist actors in Indonesia who were released from prison.”
Bashir pledged allegiance to the Islamic State in 2014 while in prison.
Eddy Hartono, of Indonesia’s terrorism agency, said Bashir would now undergo a de-radicalization program.
“We hope that Abu Bakar Bashir, after his release, will be able to deliver peaceful, soothing sermons,” he said in a statement.
In the wake of the attacks on Bali and with the support of Australia and the United States, Indonesia set up an elite anti-terrorist unit that weakened JI and led to the arrest or killing of numerous suspected militants.
But other extremist groups have since formed and carried out attacks in the world’s largest country with a majority of Muslims, and only last month did police arrest 23 militants, including Zulkarnaen.
Before the release, Bashir’s son Abdul Rohim told Reuters that his father would return to the Al Mukmin Islamic boarding school near Solo in the central province of Central Java, which Bashir founded in the 1970s and whose graduates have connected with in the past. is with militant networks and attacks.
“He has completed his term. It is purely over,” Rohim said, adding that he would hold Islamic preaching.
Security analysts say although Bashir does not exercise as much power over JI or other groups, he can still influence other militants.
“Bashir is an ideologue, his words will be followed and examples made,” said Stanislaus Riyanta, analyst.