At least 30,000 in the southern Philippines have been displaced by flash floods in two days of heavy downpour, local official said on Friday.

Ismael Mangudadatu, governor in the province of Maguindanao, told Xinhua the number of people affected came from the province including 13 low lying towns.

He said water hyacinths clogged at Rio Grande River, causing it to overflow.

"So far there were reported cases of fatalities," the governor said.

In June this year, tens of thousands of children were displaced by flash floods in the region after water lilies' unhampered spread had caused the river to overflow after days of heavy rains.

Floodwaters have submerged low lying villages in the city of Cotabato City.

Local officials warned residents in the country's southern and eastern regions of landslides and flash floods.