National Police spokesman Major General Boy Rafli Amar said one of the bodies had characteristics including a goatee and a facial mole similar to Santoso, who leads the East Indonesia Mujahideen militant group that has claimed allegiance to the Islamic State group.
"We don't want to speculate. We need to scientifically prove that it was Santoso who was shot dead," Amar said.
The shootout occurred yesterday evening and three other militants including two females escaped into the jungle. Santoso has eluded capture for more than five years.
Cabinet Secretary Pramono Anung today said police have informed President Joko "Jokowi" Widodo about the possibility Santoso was killed. He said the second of the men might be Santoso's deputy Basri, who escaped from prison in 2012. He was imprisoned in 2007 for beheading three Christian students.
More than 2,500 security forces personnel, including elite army troops, intensified their operations this year in Poso, a mountainous district of Central Sulawesi province considered an extremist hotbed, to try to capture Santoso and his followers.