Abu Wardah, better known as Santoso, is believed to be behind several terror attacks since 2012, including skirmishes with security forces during which police officers and people in Central Sulawesi were killed.
The head of the East Indonesia Mujahidin (MIT) is now the country's most wanted terrorist.
Last year, he pledged allegiance to Abu Bakr al-Baghdadi, the leader of the Islamic State in Iraq and Syria (ISIS). The Institute for Policy Analysis of Conflict had, in an April report, tagged Santoso as an ambitious, if somewhat inexperienced, terrorist.
That, however, has not stopped him from building a following, with foreign fighters, such as a group of seven Uighurs from Xinjiang in China, attempting to link up with him last year. Four were arrested but the National Police chief, General Badrodin Haiti, said on Sunday that three are believed to have made it to an MIT camp in Poso in Central Sulawesi.
Santoso used to run an Islamic bookstore before he became known as a militant.
In 2012, Santoso called himself "Abu Mus'ab Al-Zarqawi Al Indunesi", commander of the "East Indonesia Mujahidin Commandos", and declared all-out war on the Detachment 88 counter-terrorism unit, said Dr Kumar Ramakrishna, head of policy studies at the S. Rajaratnam School of International Studies, in a report then.
Sources say there is increasing concern that Santoso and the MIT may grow into a force comparable with Islamist militant groups in the southern Philippines or separatists in southern Thailand.
Francis Chan and Wahyudi Soeriaatmadja