No casualties or damage have been reported, but the volcano remained a big threat and the highest alert level was in place, said Saut Simatupang, head of Indonesia's Vulcanological Survey.
The official said smoke started emerging from the volcano on Saturday, with ash columns appearing on Monday.
"The peak of the eruption took place on Monday, when it spit volcanic ash as high as 3,500 to 4,000 metres (11,500-13,100 feet)," Simaputang said by telephone, adding that less smoke and ash had been spotted on Tuesday.
"Less smoke does not mean the volcano is safe," he said, adding that the increased activity at the volcano had been accompanied by moderate earthquakes.
Mount Gamkonora had been placed on the highest alert level of four since Monday, triggering the evacuation of nearby villages.
Some 8,400 people have already moved further away from the mountain's slopes, Simatupang said.
Another local official in the area said 4,000 people, mostly women and children, from eight villages were in temporary shelters, while some 2,000 stayed to guard their homes.
Simatupang said local flights on surrounding islands had also been affected, although longer distance flights to eastern Indonesia had not been disrupted so far.
The 1,635 metre volcano, which lies about 2,400 km (1,491 miles) east of the capital Jakarta in North Maluku province, is the highest peak on the island of Halmahera.
The last time ash and smoke streamed out of the volcano was in 1987, when no casualties were reported, although a major eruption is said to have taken place in 1673.
Indonesia has the highest number of active volcanos of any country, sitting on a belt of intense volcanic and seismic activity known as the "Pacific Ring of Fire".
(Additional reporting by Telly Nathalia)
- Reuters - Thomson Reuters Foundation
- For more humanitarian news and analysis, please visit https://www.trust.org/alertnet