Landslides and flooding have killed at least 31 people and nine others remain missing as heavy rain from the approaching Tropical Storm Nalgae lashed the southern Philippines, a disaster official said.

Torrential rainstorms unleashed flash flooding overnight that carried uprooted trees, rocks and mud into rural communities around Cotabato, a city of 300,000 people on Mindanao island.

Many residents were surprised by the rapidly rising floodwaters, Naguib Sinarimbo, civil defence chief for the regional government, said on Friday.

“The amount of rainwater that came down overnight was unusually (heavy) and flowed down mountainsides and swelled rivers,” he said, explaining that most of the victims were swept away by floodwaters and drowned, or were hit by debris-laden mudslides.

“The water started entering the houses before dawn,” Sinarimbo said, confirming that the death toll in the storm-hit areas had jumped to 31 from the earlier tally of 13.

Rescuers retrieved 16 bodies from the flood-hit town of Datu Odin Sinsuat, 10 from Datu Blah Sinsuat and five from Upi town, he told reporters.

Rescuers in rubber boats were searching flooded areas around Cotabato City and emergency teams, including military units, were also checking other areas where flooding and landslides had been reported.

Floodwaters had receded in several areas, but Cotabato remained almost entirely waterlogged on Friday and Sinarimbo said there could be more flooding because of continued heavy rain.

“Our focus at this time is rescue as well as setting up community kitchens for the survivors,” he said.

The army has deployed trucks to collect stranded residents in Cotabato and eight nearby towns, provincial civil defence chief Nasrullah Imam said.

“It was a shock to see municipalities which had never flooded getting hit this time,” he said, adding that some families were swept away when the waters hit their homes.

The state weather office in Manila said the rain storms were related to Tropical Storm Nalgae, which is headed towards the northern Philippines, and the civil defence office said nearly 5,000 people have been evacuated from flood and landslide-prone areas ahead of Nalgae’s expected landfall on Saturday or Sunday.

The Philippine Atmospheric, Geophysical and Astronomical Services Administration said that Nalgae (known locally as Paeng) is likely to intensify in the next 24 hours and would likely cause flooding and rain-induced landslides, and that winds might reach gale-force strength.

Tropical Storm Nalgae “is forecast to further intensify while moving over the warm waters of the Philippine Sea and may reach severe tropical storm category within 24 hours … it is less likely to reach typhoon category”, the agency said.