An overflowing river flooded four towns on the small island north of Sulawesi on Monday, the national disaster mitigation agency said in a statement.

"Sixteen people have been reported dead due to the flash flood," agency spokesman Abdul Muhari said, adding that teams were searching for the three missing.

He said 22 people were injured and nearly 700 villagers displaced.

"The flash flood was triggered by heavy-intensity rain that had drenched the area since the early hours, causing the river's water flow to surge suddenly," Abdul said.

Images shared by the search and rescue agency showed big rocks and uprooted trees that were swept away.

The flood cut off access to some roads and damaged dozens of homes as well as public buildings and infrastructure, the spokesman said.

Floods are common in Indonesia during the rainy season, which typically lasts between October and March.

Tropical storms and intense monsoon rains have pummelled parts of South and Southeast Asia late last year, triggering deadly landslides and floods from the rainforests of Indonesia's Sumatra to highland plantations in Sri Lanka.

Indonesian authorities say at least 1,178 people were killed in Sumatra, and more than 240,000 displaced.

While the annual monsoon season often brings heavy rain to Indonesia, the Sumatra deluge in November was among the worst disasters to strike the island since a magnitude-9.1 earthquake triggered a massive tsunami in 2004.