Santoso, who has been operating in the jungles of Sulawesi island, has been designated a special "terrorist" by the United States.
Indonesia is "99 percent" sure its most-wanted militant, a supporter of Islamic State known as Santoso, has been killed in a clash with security forces, a senior government official said on Tuesday.
"It's confirmed that Santoso ... is dead," the official, who declined to be identified, told Reuters by text message.
"This is 99 percent and was reported to the president."
Santoso, who has been operating in the jungles of Sulawesi island, has been designated a special "terrorist" by the United States. He pledged allegiance to Islamic State in 2014.
National police chief Tito Karnavian said earlier he was "90 percent" confident Santoso had been killed in the clash on Sulawesi on Monday. Central Sulawesi's police chief said authorities were getting family DNA to try to confirm the identity of the dead militant.