At least 44 people were killed and two are still missing after flash floods swept an island in Indonesia's easternmost province Sunday morning, rescue officials said.

Hours before people woke to celebrate Easter, torrential rain unleashed flash floods in the Catholic-majority Flores Island.

Mud inundated homes, while bridges and roads in the eastern end of the island were destroyed, according to National Disaster Mitigation Agency spokesperson Raditya Jati.

Rescuers are struggling to reach the remote and worst-hit area in East Flores regency.

"The only access there is by the sea from Adonara Island, but the rains -- as well as strong waves -- have prevented any crossing," Jati told AFP on Sunday.

Extreme weather is expected to continue in the coming week, he added.

Separately on Sunday, major floods also killed two people in Bima city in the neighbouring province of West Nusa Tenggara, according to the disaster agency.

Dams in four subdistricts 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 when downpours are frequent and relentless.

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

Last September, at least 11 people were killed in landslides on Borneo while a few months earlier, dozens died in landslides in Sulawesi.

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