Mount Dukono on the Halmahera island in North Maluku province erupted at 16:52 local time (0752 GMT), sending an ash tower 1.5 kilometres (0.9 miles) above its peak.
"The ash column was observed to be white to grey in colour with thick intensity towards the southwest," the volcanology agency said in a statement Wednesday.
It had followed an earlier eruption that occurred around 6:46 am local time, which the agency said spewed an ash column one kilometre into the sky.
The volcano is currently on the third-highest alert level of Indonesia's four-tiered alert system.
The agency said locals and visitors should not hike, carry out activities or approach the four-kilometre exclusion zone around Dukono's active crater.
It also urged people to prepare face masks to protect against ash falls.
"It is recommended that people around Mount Dukono always prepare masks/face and mouth covering to be used in times of need to avoid the threat of volcanic ash to the respiratory system," the agency said.
Indonesia, a vast archipelago nation, experiences frequent seismic and volcanic activity due to its position on the Pacific "Ring of Fire" where tectonic plates collide.
Last month, Mount Lewotobi Laki-Laki in Flores island shot dark ash eight kilometres into the sky, forcing thousands to evacuate and cancelling at least seven international flights from the resort island of Bali.
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