The disaster hit Agam and Tanah Datar districts in West Sumatra province at around 10:30 pm (1530 GMT) on Saturday after hours of heavy rain, triggering a flash flood and a cold lava flow from Mount Marapi, according to Basarnas search and rescue agency.
Cold lava, also known as lahar, is volcanic material like ash, sand and pebbles carried down a volcano's slopes by rain.
"Twelve people died and they had been taken to the hospital... and four other people are still being searched in Agam district," head of the local rescue agency Abdul Malik said in a statement Sunday.
Nine bodies have been identified, including those of a three-year-old and eight-year-old, he said.
"Today, we will continue the search in the two districts."
Authorities dispatched a team of rescuers and rubber boats to look for the missing victims and to transport people to shelters.
The local government set up evacuation centres and emergency posts in several spots in the two districts.
Indonesia is prone to landslides and floods during the rainy season.
In March at least 26 people had been found dead after landslides and floods hit West Sumatra.
Saturday's floods in Agam and Tanah Datar also carried cold lava down from Mount Marapi, the most active volcano in Sumatra and one of nearly 130 active volcanoes in the Indonesian archipelago.
In December, Marapi erupted and spewed an ash tower 3,000 metres (9,800 feet) into the sky, taller than the volcano itself.
At least 24 climbers, most of them university students, died in the eruption.
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