Tropical Storm Tembin hit the east coast of Mindanao, the archipelago nation's second-largest island, before dawn with gusts of 125 kilometres an hour bringing torrential rain, the state weather office said.
"We forced hundreds of people to evacuate some villages, but the water rose swiftly and our rescuers cannot reach other areas," civil defence officer Saripada Pacasum of Lanao del Sur province, one of the hardest-hit areas, told AFP.
A small landslide buried several houses in the town of Tugaya and killed two children, with five other people missing and believed trapped beneath the rubble, Pacasum said.
Another landslide buried four houses in the city of Valencia, killing an elderly woman, said the city's civil defence officer Junrey Vallejo.
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Rescuers used heavy machinery to dig in search of a girl who remained missing as of Friday afternoon, he told AFP.
Police and civil defence officials reported heavy flooding in several Mindanao towns and cities as Tembin weakened and swiftly moved across the region.
Pacasum, the provincial civil defence officer, said among the flooded areas was the city of Marawi, recovering from five months of fighting between troops and Islamic militants that left more than 1,100 people dead earlier this year.
Police also reported widespread flooding in Cagayan de Oro, one of Mindanao's largest cities.
Electricity was cut across large swathes of the island.
Tembin struck less than a week after Tropical Storm Kai- Tak devastated the central Philippines, leaving more than 54 dead and 24 missing.
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