Torrential rain sparked widespread destruction in the South East Asian neighbours, with water from overflowing dams submerging thousands of homes.
The affected area stretched from Flores island in eastern Indonesia to East Timor.
More than 40 people are still missing in Indonesia, and officials warn the death toll could rise further.
“There are 55 dead, but this number is very dynamic and will definitely change, while some 42 people are still missing,” Indonesian Disaster Mitigation Agency spokesperson Raditya Djati told broadcaster MetroTV.
“The mud and the extreme weather have become a serious challenge and the debris piling up has hampered the search and rescue team,” Mr Djati said of the situation in Indonesia.
“We suspect many people are buried but it’s not clear how many are missing,” his colleague Alfons Hada Bethan, head of the East Flores disaster agency, said.
“The evacuees are spread out. There are hundreds in each sub district but many others are staying at home. They need medicine, food, blankets.”