Firebrand preacher Abu Bakar Bashir has arrived home after more than a decade behind bars as Prime Minister Scott Morrison declared his release from jail as deeply distressing.
And the Australian government has warned Indonesia he should not be allowed to use his freedom to incite violence.
The 82-year-old was released early on Friday from Gunung Sindur Prison in Bogor, West Java and with his sons and lawyers, drove in convoy to his home in Solo in Central Java.
Bashir and his family and supporters then immediately went to the mosque for prayers and he posed for photographs, sitting in a wheelchair and with a face mask.
He had earlier walked out of prison aided by a walking stick, appearing frail.
The man, believed to have been the spiritual leader of Indonesian terror group Jemaah Islamiyah, was freed at the expiration of his 15-year sentence on terrorism offences. He had earned 55 months of remissions.
Bashir was serving a sentence in relation to funding for a terrorist training camp in Aceh but a conviction in relation to the 2002 Bali bombing was overturned in 2006 and no charges in relation to that bombing have stuck against Bashir.
"This is very distressing to the friends and families of the Australians, the 88 Australians, who were killed in the Bali bombings of 2002 ... It's hard, and it's gut-wrenching, having spent time with the families of those victims, of that terrible bombing," Mr Morrison said on Friday.
"We have always called for those who were involved - not just I as prime minister, my predecessors of all political persuasions - to face tougher, proportionate and just sentences in these cases. Decisions on sentences, though, as we know, are a matter for the Indonesian justice system. We have to respect the decisions that they take.
"We have made clear through our embassy in Jakarta the concerns we have that such individuals be prevented from further inciting others, and we will continue to follow those sort of issues through.
"They have been released consistent with the Indonesian justice system. That doesn't make it any easier for any Australian to accept that, ultimately. That those who are responsible for the murder of Australians would now be free. It's sometimes not a fair world."
Opposition leader Anthony Albanese said it was a difficult day for the families.
"My heart goes out to all those who will be doing it tough today. And I would hope that the Australian government, I'm sure, are making strong representations to make sure that the closest eye is kept on this bloke to make sure that his activities don't further the, quite frankly, catastrophic human consequences of his ideological position."
The 82-year-old left the Bogor prison accompanied by his two sons, a doctor and lawyer.
Rika Aprianti, from Indonesia's Corrections Directorate General said the release was conducted at 5.20am to minimise crowds and avoid any health issues related to the COVID-19 pandemic.
As he left the prison, Bashir thanked prison staff. "I would like to say many thanks and hopefully God will reward you that have already helped me all this time."
Bashir's lawyer, Ahmad Michdan, told AAP that Bashir had been COVID-19 tested and was negative before his release and a full medical check conducted.