Eight people managed to escape when water engulfed the boat early yesterday on remote Siau island during a tropical downpour, the official said, in an area hit by deadly landslides and floods in recent weeks.
"The flood was so strong that it capsized a small boat on the coast of Siau," Bagus Tjahjono, a senior official at the national disaster agency, told AFP.
It was not clear what type of vessel was involved in the accident but boats are commonly used for transport in the area.
Sulawesi has also been badly hit. Yesterday one person died when floods swept away his riverside house, while a second died in hospital from injuries sustained in earlier flooding.
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The latest deaths on Siau and Sulawesi take the toll from flooding and landslides in the area in recent weeks to 23, according to the disaster agency.
Flooding and landslides occur frequently across Indonesia during the six-month rainy season.
Disaster agency spokesman Sutopo Purwo Nugroho said an average of 541 people have died every year from floods and landslides in the sprawling archipelago over the past decade.