There were 55 people dead and 40 missing in Indonesia's East Nusa Tenggara province, after the cyclone brought flash floods, landslides and strong winds amid heavy rain since the weekend, disaster agency BNPB said.
More than 400 people were evacuated and thousands more impacted, it said.
In East Timor, which shares the Timor island with Indonesia, 21 people were killed by landslides, flash floods and a falling tree, mostly in the capital Dili.
More than 1,500 people were evacuated, Main Director of Civil Protection, Ismael da Costa Babo, told reporters.
Several bridges collapsed, trees fell and blocked some roads in Indonesia and at least one ship sank in high waves triggered by the cyclone, complicating search and rescue operations, BNPB said.
Agustinus Payong Boli, deputy head of the East Flores government, said rescuers halted evacuations because a storm was still raging and they needed heavy equipment.
In Lembata, where at least 20 people died, authorities feared bodies had been washed away.
"We are using rubber boats to find bodies at sea. In several villages, flash floods hit while people were sleeping," Thomas Ola Langoday, deputy head of
Lembata district government, told Reuters by phone.
President Joko Widodo offered his condolences and urged residents to follow the direction from field officers during extreme weather.
The Seroja cyclone hit the Savu sea southwest of Timor island in the early hours of Monday, Indonesia's weather agency said.