The victims included a seven-year-old girl and a one-year-old boy, as well as their mother.
Landslides caused by sustained torrential rains in Bali hit three villages destroying homes and villages late Thursday night, and taking lives along the way.
Local disaster agency officials said villagers had been evacuated from the affected areas, which are far from the popular beach resorts in the south of the island, and no one else was believed to be missing.
In nearby Awan village, four people were killed, while in Sukawarna another person died, Bali Red Cross operational chief Putu Dedy Rimbawan said.
The disaster board has warned that heavy rain is likely to continue to fall on the region and has warned people to be cautious of landslides, floods and hurricanes.
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The country's Disaster Mitigation Agency confirmed 12 people were killed, with young children among the dead.
Heavy downpours were blamed for the disaster in Bulurejo village of Karanganyar district, Risky A, senior official at the provincial disaster management agency said.
Rains often cause flooding and landslides in Indonesia, an archipelago where millions of people live in mountainous areas or on flood plains near rivers.
At least 13 people have been killed and thousands more made homeless after devastating floods swept across Indonesia.
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