National Disaster Mitigation Agency spokesperson Raditya Jati said floods brought by intense rains caused floodwaters as high as 3 meters (10 feet).
As of Sunday, 39,549 people had been evacuated and at least 15 had been killed due to floods that affected 10 districts and cities in South Kalimantan province on Borneo island.
Separately, five people were killed and 500 others were evacuated after floods and landslides in Manado city in North Sulawesi province on Saturday. One other person was missing.
Seasonal rains and high tides in recent days have caused dozens of landslides and widespread flooding across much of Indonesia, a chain of 17,000 islands where millions of people live in mountainous areas or near fertile flood plains close to rivers.