As Usagi -- the archipelago nation's fifth storm in three weeks -- headed north to Taiwan, rescuers worked to reach residents stranded on rooftops in northern Luzon island, where herds of livestock were devastated.
The recent wave of disasters has killed at least 159 people and prompted the United Nations to request $32.9 million in aid for the worst-affected regions.
On Thursday, flash floods driven by Usagi struck 10 largely evacuated villages around the town of Gonzaga in Cagayan province, local rescue official Edward Gaspar told AFP by phone.
"We rescued a number of people who had refused to move to the shelters and got trapped on their rooftops," Gaspar added.
While the evacuation of more than 5,000 Gonzaga residents ahead of the typhoon saved lives, he said two houses were swept away and many others were damaged while the farming region's livestock industry took a heavy blow.
"We have yet to account for the exact number of hogs, cattle and poultry lost from the floods, but I can say the losses were huge," Gaspar said.
Trees uprooted by flooding damaged a major bridge in Gonzaga, isolating nearby Santa Ana, a coastal town of about 36,000 people, Cagayan officials said.
"Most evacuees have returned home, but we held back some of them. We have to check first if their houses are still safe for habitation," Bonifacio Espiritu, operations chief of the civil defence office in Cagayan, told AFP.
By early Friday, Usagi was over the Luzon Strait with a reduced strength of 120 kilometres (75 miles) an hour as it headed towards southern Taiwan, where authorities had downgraded the typhoon to a tropical storm.
But the streak of violent weather was forecast to continue in the central Philippines, where Severe Tropical Storm Man-yi is set to reach coastal waters by Sunday.
The weather service said it could potentially strike at or near the heavily populated capital Manila.
A UN assessment said the past month's storms damaged or destroyed 207,000 houses, with 700,000 people forced to seek temporary shelter.
Many families were without essentials like sleeping mats, hygiene kits and cooking supplies, and had limited access to safe drinking water.
Thousands of hectares of farmland were destroyed and persistent flooding was likely to delay replanting efforts and worsen food supply problems, the report added.
About 20 big storms and typhoons hit the Southeast Asian nation or its surrounding waters each year, killing scores of people and keeping millions in enduring poverty, but it is unusual for multiple such weather events to take place in a small window.
The weather service said this tends to happen during seasonal episodes of La Nina, a climatic phenomenon in the Pacific Ocean that pushes more warm water toward Asia, causing heavy rains and flooding in the region and drought in the southern United States.
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