Mount Sinabung, in the north of the island of Sumatra, began erupting around midnight after rumbling for several days, prompting some villagers to panic before the mass evacuation got under way.
Indonesia is on the so-called Pacific Rim of Fire, an arc of volcanoes and geological fault lines triggering frequent earthquakes around the Pacific Basin. The eruption triggered the highest red volcano alert.
Two people died, one from breathing problems and the other from a heart attack, and two suffered injuries in road accidents as trucks, ambulances and buses were mobilised in the rescue operation.
"This is the first time since 1600 that Sinabung has erupted and we have little knowledge in terms on its eruptive patterns," said Surono, head of Indonesia's vulcanology center.
Authorities took at least 12,000 people from high risk areas on the slopes of the 2,460-meter volcano to temporary shelters. Local TV showed showed women and children wearing face masks in cramped tents.
The area around the volcano is largely agricultural.
"Since this is the first eruption we've had in Sinabung, we're anticipating residents to remain at the shelters for at least a week while waiting for further status alert," said Priyadi Kardono, a spokesman at the national disaster management agency.
Residents panicked when the volcano started erupting overnight and some of them who live in safer areas chose to take refugee at shelters, Kardono added.
The eruption has not damage roads or bridges. The nearest big city is Medan where there were no disruptions to flights.
