In Jakarta, waters were receding after days of heavy rain caused flooding in some areas, displacing more than 60,000 people, said an official at the capital's disaster management agency, Basuki Rachmat.
At least 11 people in Jakarta have been killed since last week, mostly from drowning and electrocution, he said.
The national weather service has warned Jakartans to brace for more floods as the rainy season is expected to last until February.
In North Sulawesi province, the death toll from floods and landslides that hit six districts and towns has risen to 19, with nearly 20,000 people displaced, said National Disaster Management Agency spokesman Sutopo Nugoroho.
More than 700 people were injured.
Floods and landslides are common during the rainy season in Indonesia.