Torrential rain unleashed flash floods in the island hours before people woke up.
Mud inundated homes, while bridges and roads in the eastern end of the island were destroyed, according to Indonesia’s National Disaster Mitigation Agency (NDMA).
Rescuers are struggling to reach the remote and worst-hit area in East Flores regency.
The only access there is by the sea from Adonara Island, but the rains, as well as strong waves, have prevented any crossing, NDMA spokesperson Jati said, adding that extreme weather is expected to continue in the coming week.
Separately on the same day, major floods also killed two people in Bima city in the neighbouring province of West Nusa Tenggara, according to the disaster agency.
Dams in four sub-districts also overflowed, submerging nearly 10,000 houses in Bima following hours of downpour, said Jati.
Fatal landslides and flash floods are common across the Indonesian archipelago during the rainy season when downpours are frequent and relentless.
In January, flash floods damaged the Indonesian town of Sumedang in West Java, killing 40 people.
The NDMA has estimated that 125 million Indonesians – nearly half of the country's population – live in areas at risk of landslides.