More than 50 people were killed after flash floods and landslides swept through eastern Indonesia and neighbouring Timor Leste on Sunday, authorities said, warning the toll could rise further.

Floods sparked by torrential rain wreaked havoc and destruction on islands stretching from Flores Island in Indonesia to Timor Leste, a small nation east of the Indonesian archipelago.

The deluge and subsequent landslides caused dams to overflow, submerging thousands of houses and leaving rescue workers struggling to reach survivors trapped in the aftermath.

"Four sub-districts and 7 villages have been impacted. After verifying the data with our team in the field, we found that there are 41 people dead," Indonesian Disaster Mitigation Agency spokesperson Raditya Jati told journalists, revising down earlier figures.

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Floods sparked by torrential rain wreaked havoc and destruction on islands stretching from Flores Island in Indonesia to Timor Leste, a small nation East of the Indonesian archipelago Photo: AFP / VALENTINO DARIEL SOUSA

"27 people are still missing and nine people are injured," he added.

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.

In neighbouring Timor Leste, 11 were killed by floods in the capital Dili, authorities said.

"We are still searching for the areas impacted by the natural disasters," Secretary of State for Civil Protection for Timor Joaquim Jose Gusmao dos Reis Martins told journalists.

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Debris was left behind in the town of Adonara in East Flores after flash floods and landslides swept eastern Indonesia and neighbouring East Timor Photo: AFP / Joy Christian

The death toll and the number of injured victims could still rise, authorities warned.

East Flores deputy regent Agustinus Payong Boli estimated there were 60 casualties in his municipality.

"The majority of them, 55, are in Lemanele village. Many people died here because the village was hit by both landslides and flash floods," he told AFP, providing numbers not yet confirmed by national authorities.

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Heavy rains and strong winds also lashed East Timor's capital Dili, causing extensive flooding Photo: AFP / VALENTINO DARIEL SOUSA

Images from Lemanele showed engulfed houses, debris covering entire roads, fallen trees and damaged power lines.

In Lembata, an island halfway between Flores and Timor, parts of affected villages were displaced down a mountain slope and near the coastline, according to an AFP journalist on the scene.

Road access has been cut off and local officials were forced to deploy heavy equipment to reopen the roads.

Injured victims have been evacuated to neighbouring villages that were unaffected by the flash floods, as well as local hospital and health facilities.

Images from Lembata showed barefoot locals wading through mud evacuating victims on makeshift stretchers surrounded by collapsed houses.

Separately on Sunday, two people were killed in major floods 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 a nine-hour downpour, said Jati.

Fatal landslides and flash floods are common across the Indonesian archipelago during the rainy season.

January saw flash floods hit the Indonesian town of Sumedang in West Java, killing 40 people.

And last September, at least 11 people were killed in landslides on Borneo.

The country's disaster agency has estimated that 125 million Indonesians -- nearly half of the country's population -- live in areas at risk of landslides

The disasters are often caused by deforestation, according to environmentalists.

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