At least 71 people have died after flash floods and landslides hit Indonesia and East Timor on Sunday.

Torrential rain sparked widespread destruction in the South East Asian neighbours, with water from overflowing dams submerging thousands of homes.

The affected area stretched from Flores island in eastern Indonesia to East Timor.

More than 40 people are still missing in Indonesia, and officials warn the death toll could rise further.

"There are 55 dead, but this number is very dynamic and will definitely change, while some 42 people are still missing," Indonesian Disaster Mitigation Agency spokesperson Raditya Djati told broadcaster MetroTV.

"The mud and the extreme weather have become a serious challenge and the debris piling up has hampered the search and rescue team," Mr Djati said of the situation in Indonesia.

"We suspect many people are buried but it's not clear how many are missing," his colleague Alfons Hada Bethan, head of the East Flores disaster agency, said.

"The evacuees are spread out. There are hundreds in each sub district but many others are staying at home. They need medicine, food, blankets."

At least 21 people have also died in East Timor, also known as Timor Leste, news agencies quoted officials in the island nation as saying.

Many of the victims are believed to be from the country's capital Dili.

Indonesian president Joko Widodo has offered his condolences and urged people to follow the advice from officials during extreme weather periods.

"I have ordered for disaster relief efforts to be conducted quickly and well, for example for health service assistance, availability of logistics and basic needs for the displaced and the reparation of infrastructure," he said.