Mount Ibu, located on the island of Halmahera in North Maluku province, erupted Thursday morning shortly after 1:00 am (1600 GMT Wednesday) and then again at 7:46 am and 8:11 am, the agency said.
The initial eruption spewed an ash tower more than 5,000 metres (16,400 feet) above the peak, according to a statement on the agency's website.
The latter eruption lasted around two minutes and caused an ash column that "was observed around 1,000 metres above the peak," Geological Agency head Muhammad Wafid said in the statement.
The agency advised residents and tourists to stay out of an exclusion zone between four and seven kilometres from Ibu's crater and to wear eye and mouth coverings when outdoors.
The eruptions were the latest in a series of huge belches that forced authorities to evacuate more than half a dozen villages last month.
The latest eruptions caused no new evacuation orders and there were no immediate reports of casualties or damage on Halmahera, which hosts around 700,000 people.
Ibu is one of Indonesia's most active volcanos, erupting more than 21,000 times last year. It remains at the highest alert level in a four-tiered system.
Indonesia, a vast archipelago nation, experiences frequent seismic and volcanic activity due to its position on the Pacific "Ring of Fire".
In April, Mount Ruang in North Sulawesi Province erupted more than half a dozen times, forcing thousands of residents of nearby islands to evacuate.
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