“It was a shock to see municipalities which had never flooded getting hit this time,” Imam said, adding that some families were swept away when the waters hit their homes.
The heavy rainfall began late Thursday in the impoverished region, which is under Muslim self-rule after decades of separatist armed rebellion.
The state weather office in Manila said it was partly caused by Tropical Storm Nalgae, which it expects to strengthen at landfall.
Nalgae was now heading toward the northern or central sections of the Philippines, with the state weather service saying it was not ruling out a landfall on Samar island later Friday, much earlier than earlier forecast.
Nearly 5,000 people were evacuated from flood and landslide-prone communities in these areas, the civil defence office said.
The coast guard also suspended ferry services in much of the archipelago nation where tens of thousands of people board boats each day.
An average of 20 typhoons and storms strike the Philippines each year, killing people and livestock and destroying farms, houses, roads and bridges, although the south is rarely hit.
Scientists have warned that storms are becoming more powerful as the world gets warmer because of climate change.