The bulk of the casualties were in Sumatra's northern Aceh province, with the number in the main city of Banda Aceh accounting for at least 3,000.
Wawan Setiawan, a spokesman for the Social Affairs ministry, warned the toll could still continue to climb with unconfirmed reports of up to 5,000 dead in Banda Aceh alone.
The Detikcom online news service reported that about 700 soldiers involved in a major military campaign in Aceh were missing. The troops had been waiting in Banda Aceh's port to be shipped out of the region.