Mud rolled down from surrounding hills shortly after midnight and struck almost 50 houses in Lamenele village on Flores Island in East Nusa Tenggara province.
In another village, Waiburak, three people were killed and seven remained missing when overnight rains caused rivers to burst their banks, sending muddy water into large areas of East Flores district, Ola said.
At least 21 people have also died in East Timor, also known as Timor Leste, news agencies quoted officials in the island nation as saying.
"There are 44 people dead with nine injured" in East Flores regency, and "many (.) are still under the mud", National Disaster Mitigation Agency spokesperson Raditya Jati told AFP.
Dams in four sub-districts also overflowed, submerging almost 10,000 houses in Bima following a nine-hour downpour, said Jati.
Mud inundated homes, bridges and roads in the East Flores municipality, where rescuers struggled to reach a remote and badly-hit area because of rains and strong waves.
Tropical Cyclone Seroja has produced high waves, strong winds and heavy rains for the past three days and its effects were expected to last until Friday, said Dwikorita Karnawati, the head of Indonesia's Meteorology, Climatology and Geophysical Agency.
He said more than 1,500 people have been evacuated to shelters in the capital Dili.
"The evacuees are spread out". More than two dozen others were still missing.
"They need medicine, food, blankets".
Pounding rains challenged efforts to find any survivors.
Earlier, road access had been cut off and local officials were forced to deploy heavy equipment to reopen the roads.
Images from the island showed barefoot locals wading through mud and past collapsed houses to evacuate victims on makeshift stretchers.
Residents inspect the damage at a village hit by flash flood in East Flores, Indonesia, Sunday, April 4, 2021.
In January this year, 40 people died when flash floods hit the town of Sumedang on Java.
The country's disaster agency has estimated that 125 million Indonesians - almost half of the country's population - live in areas at risk of landslides.
The country's disaster agency has estimated that 125 million Indonesians - almost half of the country's population - live in areas at risk of landslides The disasters are often caused by deforestation, according to environmentalists.