Two of the fatalities, a one-year-old girl and a 65-year-old man, died from hypothermia, while a 35-year-old pregnant woman was also reported to have died.
The storm has also caused flooding and significant damage to the local infrastructure.
Hagupit, dubbed "Ruby" by the Filipino authorities, is moving west-northwest at 10 kph, and thus it will not leave the Philippines and move out over the South China Sea until Tuesday or Wednesday, according to the Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA), the Filipino weather service.
Although sustained winds from the storm weakened from 185 kph to 140 kph since its landfall Saturday in the town of Dolores, its slow speed through the region has resulted in huge amounts of rain being dumped in the area, causing extensive flooding.
In addition, the rains could cause mudslides, experts said -- a possibility that particularly worries the authorities in Albay, in the eastern Philippines, where the Mayon Volcano is located and where significant mudslides have already cut off several towns.
Mayon has expelled a large amount of volcanic material in recent months that, due to the effect of the rain and winds, could slide down the hills onto the nearby villages.
PAGASA declared a level 1 alert Saturday night in densely-populated Manila, where heavy rain and a storm surge of one to two metres is expected.
In the greater capital area, where some 12 million people live, schools have been closed down, just as in 30 other provinces around the country.
Six airports remain closed in the archipelago, while the local airlines announced the cancellation of more than 183 flights.
Around 15 to 20 typhoons hit the Philippines each year during the rainy season, which generally begins in June and lasts until November.
Philippine typhoon death toll exceeds 5200 govt