At least 100 rescuers, military and police personnel, as well as two thermal drones, were deployed to find the two Singaporeans and one Indonesian, Iwan Ramdani, the head of the local rescue agency, told Reuters on Saturday.
Survivors told police that three people died in Friday's eruption, local police chief Erlichson Pasaribu said, but the rescue agency had not confirmed the deaths by Saturday.
The volcano in North Maluku province began erupting on Friday morning, spewing ash as high as 10km into the sky, Indonesia's volcanology agency said.
"We are focusing the search around the crater, covering an area around 700 metres," Iwan said.
Authorities on Friday evacuated 17 people - seven Singaporeans and 10 Indonesians.
The rescue agency had halted the search on Friday evening as the volcano continued to erupt.
Saturday's search remained hampered, Iwan said, as the volcanology agency reported at least four morning eruptions.
Singapore's Ministry of Foreign Affairs and embassy in Jakarta were working with the Indonesian authorities to gather information and provide consular assistance and support to the affected Singaporeans and their families, the ministry said in a statement.
The volcanology agency is maintaining the third-highest alert level for Mount Dukono, said Lana Saria, the agency's head, adding that residents and tourists were advised not to do any activities within four kilometres of the crater.
There were no reports of flight disruptions caused by the eruption.
Indonesia sits on the Pacific's Ring of Fire, an area of high seismic activity atop various tectonic plates.
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