Two people died in nearby West Nusa Tenggara province.
There were also concerns about possible COVID-19 infections in crowded evacuation centres.
In neighbouring East Timor, at least 33 were killed in floods and landslides and by falling trees. Civil defence authorities were using heavy equipment to search for survivors.
"The number of victims could still increase because many victims have not been found," the main director of civil protection, Ismael da Costa Babo, told Reuters.
"They were buried by landslides and carried away by floods."
Some residents of Lembata island may have also been washed away by mud into the sea.
A volcano that erupted on Lembata last month wiped out vegetation atop the mountain, which allowed hardened lava to slide towards 300 houses when the cyclone struck, a senior district official said, hoping help was on the way.
"We were only able to search on the seashore, not in the deeper area, because of lack of equipment yesterday," Thomas Ola Langoday told Reuters by phone.
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He feared many bodies were still buried under large rocks.
President Joko Widodo urged his cabinet to speed up evacuation and relief efforts and to restore power.
Weather agency head Dwikorita Karnawati said once-rare tropical cyclones were happening more often in Indonesia and climate change could be to blame.
"Seroja is the first time we're seeing tremendous impact because it hit the land. It's not common," she said.
