Rescuers are trying to deliver aid, but high waves and severe weather conditions are hampering efforts to reach the worst-affected island.
At least 55 people were killed after flash floods and landslides struck Indonesia on Sunday, rescue officials said. At least 21 people have also died from the floods in the tiny half-island nation of East Timor.
Worst hit was East Flores regency in Indonesia's southernmost East Nusa Tenggara province.
Authorities expect the death toll to rise.
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Rescuers recovered the bodies of 38 people who died when mud slid onto dozens of houses in Lamenele village on Flores Island in East Flores, said Lenny Ola, who heads the regional disaster agency.
The bodies of three people were found after being swept away by flash floods in Oyang Bayang village as 40 houses were destroyed, she said.
In Waiburak village, three people were killed and seven remained missing when rivers burst their banks, Ola said.
Four injured people were being treated at a local health clinic.
Hundreds of people were displaced after leaving submerged homes. Some homes were carried off by the floodwaters.
The rainfall and floods have also caused power cuts, blocked roads and cut off bridges.
Meanwhile, nine hours of rainfall wreaked havoc in Bima, a town in the neighboring province of West Nusa Tenggara.
The heavy rain caused dams in four subdistricts to overflow, submerging nearly 10,000 houses, Jati said.
Hampered rescue efforts
Aid and relief efforts for the affected villages were hampered by the absence of transportation to Flores island, which was hardest hit.
It can only be reached by sea, but links have been suspended because of high waves and severe weather conditions.
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"We are working on other ways to reach the island other than by the sea," said Raditya Jati, a spokesperson for the National Disaster Mitigation Agency.
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Fatal landslides and flash floods are common across the Indonesian archipelago during the rainy season.