The military and rescue officials have been deployed to the four affected areas in North Sumatra province.
"In total, 16 people died and seven more people are missing," the spokesman of the National Disaster Mitigation Agency or BNPB, Abdul Muhari, said in a statement Monday.
Karo district suffered from the most casualties with five people killed and five more still missing after floods hit a resort area on Saturday.
The rest of the victims are spread in three other districts in the province: Deli Serdang, South Tapanuli, and Padang Lawas.
Homes, mosques, and public facilities were also damaged.
Muhari said Deli Serdang and Karo have been repeatedly hit by flash floods and landslides.
"This year alone, these two districts have been hit by disaster three times and twice respectively," he said.
He warned Indonesians to avoid visiting outdoor tourism spots in areas near water during the rainy season.
Indonesia has suffered a string of recent extreme weather events, which experts say are made more likely by climate change.
In May, at least 67 people died after a mixture of ash, sand, and pebbles carried down from the eruption of Mount Marapi in West Sumatra washed into residential areas, causing flash floods.
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