The members of the mostly Muslim ethnic minority were killed in a shootout yesterday morning in mountains on the island of Sulawesi, as authorities hunted for the radical group's leader.
"We can confirm that the two who died were Uighurs," Central Sulawesi police chief Rudy Sufahriadi told AFP.
The Uighurs were fighting alongside Santoso, who leads the Eastern Indonesia Mujahideen, a group that has been waging a guerrilla campaign against authorities from remote bases in the jungles and mountains.
Sufahriadi said that based on testimony from detainees, there are four more Uighurs still fighting with Santoso's group. The group itself is estimated to have some 30 fighters to 40 fighters, he said.
Several Uighurs have joined radicals in Indonesia in recent years. A few months ago, police detained a Uighur man on the outskirts of Jakarta who they suspect planned to launch a suicide bombing attack.
Last year, an Indonesian court jailed four Uighurs for attempting to join Santoso's group.
Many are believed to have fled the restive region in recent years, sometimes travelling through Southeast Asia in the hope of resettling in Turkey.
Indonesia, the world's most populous Muslim-majority nation, has suffered a string of Islamic militant attacks in the past 15 years.
The latest was a deadly suicide bombing and gun assault in Jakarta in January, which was the first major attack for seven years and was claimed by the Islamic State (IS) group.
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