Searchers on Sunday found the bodies around the crater rim, and evacuation was under way, local rescue agency head Iwan Ramdani told Reuters.
"Evacuation of the bodies is still hampered by eruptions that continue to occur and bad weather," Iwan said, adding rain was falling in the area.
Some 150 personnel with two thermal drones had been deployed since Sunday morning with the focus of the search around 100-150 metres of the crater rim.
Mount Dukono, located in North Maluku province bordering the Pacific Ocean, began erupting on Friday, spewing ash as high as 10km. It has continued to erupt at a lower scale ever since.
Before discovering the bodies, rescuers found backpacks suspected to belong to the two Singaporeans. Survivors told police they were dead, police chief Erlichson Pasaribu had said.
Authorities on Saturday confirmed that one Indonesian hiker who had previously gone missing was also dead.
Seventeen people, including seven Singaporeans and 10 Indonesians, survived the incident.
The Singaporeans will travel home on Sunday, Singapore's Foreign Ministry said in a statement.
It was unclear when the bodies of the two who died will be returned.
Indonesia's volcanology agency reported at least three eruptions as of Sunday morning, with the highest spewing 1.3km of volcanic ash, it said in a statement.
The agency is still maintaining the third-highest alert level for Mount Dukono and bans any activities within four kilometres of the crater.
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