Extreme weather in two provinces has damaged hundreds of houses and left scores homeless, officials said on Thursday.

On the East Nusa Tenggara island of Flores on Wednesday, high waves that reached as far as 100 meters inland swept away at least 18 houses in Sikka district's Nangahale village, said Fransiska Palan Bolen, secretary of the province's Natural Disaster Management Agency (BNPD).

No injuries were reported in the incident.

Fransiska said the affected villagers had been evacuated to emergency camps and that her office had sent personnel, supplies and food to help the victims.

"We have made it a priority, flying the aid to Maumere so that it can be distributed immediately," Fransiska said from the provincial capital, Kupang.

A Sikka district counselor, Siflan Angi, said the government would build embankments to protect the area from further high waves.

Residents have also been warned to temporarily suspend their fishing activities because of the high waves.

In the East Kupang subdistrict of Kupang city, strong winds left at least a dozen families homeless.

The early morning storm destroyed 11 houses, built by the military in 2006 to house refugees from East Timor.

There were no injuries and the government deployed 23 personnel to help the victims.

Gasper Fernandez, one of the victims, told the Jakarta Globe he was asleep when the storm struck.

"Luckily were able to escape before our house collapsed," he said.

In Kupang's Oepura subdistrict, a landslide struck 10 houses but there were no casualties reported.

Eston Foenay, the deputy mayor of Kupang, visited the subdistrict, taking with him 250 kilograms of rice to distribute to affected families.

Mikhael Tennis, one of the victims, said the landslide followed three days of heavy rain.

The Climatology, Meteorology and Geophysics Agency (BKMG) said extreme weather in Kupang was expected to continue for at least the next three days and possibly for another week.

"It all depends on the development of a tropical cyclone called Fince," Kukuh Ribudiyanto, head of the extreme weather early warning division at the agency, said on Thursday.

Kukuh said the cyclone would affect the intensity of storms in the region as well as the size of the waves.

"Heavy rainstorms accompanied by strong winds are expected, and it is possible that waves could reach more than three meters in height," he said.

He said the cyclone was traveling east from the southern area of the Java Sea.

"The La Nina influence could make the conditions even worse by prolonging the rainstorms," he added.

Meanwhile, in the Pakem subdistrict of Bondowoso, East Java, strong whirlwinds damaged at least 546 houses, a district official said on Thursday.

Abdurrahman, head of the Bondowoso Disaster Management Office (BPBD), told Antara state-run news agency that whirlwinds swept through four villages in Pakem - Kupang, Andongsari, Gadingsari and Petung - on Wednesday.

Abdurrahman said that 92 houses were heavily damaged, 263 were moderately damaged and 191 suffered light damage.

However, he said there were no serious casualties reported. "Three people received minor injuries when their houses toppled over. They were treated at a local public health center," he said.

The Bondowoso BPBD has been distributing food supplies and other aid to the affected people since Wednesday evening.

"Today we distributed 2.5 tons of rice," Abdurrahman said.