The death toll from floods on Indonesia's Sulawesi island has risen to at least 21, authorities said Wednesday as residents tried to salvage a few belongings from their inundated homes.

The flash floods in North Luwu regency left hundreds of houses buried in mud after three rivers burst their banks due to torrential rains which started on Monday.

Nearly 1,600 people were taking refuge in temporary shelters, the Search and Rescue Agency said Wednesday.

The death toll rose to 21 with the discovery of six more bodies including a child but authorities said it was not clear how many people were still missing.

Dozens thought to have been swept away had been located but at least two remained unaccounted for.

"The number of missing people might increase as many villages haven't reported exact data of their missing residents," said the agency's chief in South Sulawesi, Muhammad Rizal.

Putri Nirmala Pakaya, whose three-year-old daughter was missing, pleaded with officials to help find her child who was swept out of her father's arms by the floods.

"We were sleeping when the floods suddenly hit our house hard three times. The third time, our house collapsed," she told AFP on Wednesday.

Putri, her husband, and her five-month-old son survived although she suffered a fractured leg.

Hundreds of houses as well as government offices and public facilities were engulfed mud from the floods. 

Villagers searched through their homes for pots and pans and other belongings to take to the temporary shelters.

Adi Maulana, a geologist at Hasanuddin University, said North Luwu district was a flood-prone area since the 1800s.

"The North Luwu regency is indeed prone to floods because the distance between the plains and mountains is very close. So, if the upstream area is not well-conserved, flooding will certainly come every rainy season," said Adi, who is also the head of the university's disaster study centre.

Earlier this year, record rains triggered flooding and landslides that killed nearly 70 people in and around Indonesia's capital Jakarta, which is on neighbouring Java island.

The Southeast Asian archipelago is regularly hit by floods during the rainy season.