Two missing Singaporeans have been confirmed dead following the eruption of Mount Dukono on Indonesia's remote Halmahera island.

Heng Wen Qiang Timothy, 30, Shahin Muhrez bin Abdul Hamid, 27, and an Indonesian woman died when Mount Dukono erupted on Friday, the local authorities said.

The bodies of the Singaporeans were found around the carter rim, and an evacuation mission was underway on Sunday, said Iwan Ramdani, the head of the local rescue agency. Backpacks suspected to belong to the two Singaporeans were also recovered by a group of rescuers.

"Evacuation of the bodies is still hampered by eruptions that continue to occur and bad weather," Mr Iwan said.

The body of the Indonesian woman was recovered on Saturday and sent to a regional hospital for identification.

About 20 climbers had set out on Thursday to ascend the nearly 1,355m volcano in defiance of safety restrictions, according to the North Halmahera police.

They became stranded when Dukono erupted at 7.41am local time, spewing a thick ash column that rose about 10km above the summit. The eruption was recorded on seismographs for more than 16 minutes, Indonesia’s Geological Agency said.

“They were aware that climbing was prohibited as the mountain is a restricted zone due to its high alert status, but insisted on going ahead,” police chief Erlichson Pasaribu told reporters.

Seventeen climbers had been safely evacuated, including seven Singaporean nationals and two Indonesians who joined the rescue operation and provided information on climbing routes of the victims before the eruption. Five of those evacuated were reported injured.

A team of 150 personnel and two thermal drones were deployed on Sunday morning for the search operation.

The police chief said multiple local guides were being investigated and could face possible legal action for bringing the hikers close to the crater despite it being closed.

"The guides are currently under investigation for alleged negligence resulting in another person's death," Mr Erlichson told CNA.

The Center for Volcanology and Geological Hazard Mitigation has long banned activities within a 4km danger zone radius of Dukono’s crater, citing hazards such as volcanic explosions, ashfall and toxic gases.

Despite warnings on social media and signs at the site, “many people remain determined to climb, driven by the desire to create online content,” Mr Erlichson earlier said.

Mount Dukono is one of Indonesia’s most active volcanoes and has been erupting almost continuously since 1933. Indonesia sits along the Pacific “Ring of Fire,” an area of intense seismic and volcanic activity, and is home to more than 120 active volcanoes.

Authorities also have warned of possible secondary hazards, including volcanic mudflows, especially during heavy rain, which could travel along rivers flowing from the volcano’s slopes.

Volcanic activity at Dukono remains high, and authorities said it was at the second-highest alert level. Authorities said the volcano has shown an increase in explosive magmatic eruptions since late March, with an average of about 95 eruptions a day.