The typhoon roared in from the Pacific Ocean and crashed into remote fishing communities of Samar island on Saturday night with wind gusts of 210kms an hour, local weather agency Pagasa said, and continued to tear through the country into Sunday morning.
The wind strength made Hagupit the most powerful storm to hit the Philippines this year, exceeding a typhoon in July that killed more than 100 people.
"Tin roofs are flying off, trees are falling and there is some flooding," Stephany Uy-Tan, the mayor of Catbalogan, a major city on Samar, told the AFP news agency.
According to reports from news agencies and local media, close to a million people had fled to shelters in areas along the path of the typhoon.
Fearful of a repeat of last year when Super Typhoon Haiyan claimed more than 7,350 lives, the government undertook a massive evacuation effort ahead of Hagupit that saw millions of people seek shelter.
Hagupit was forecast to take days to cut across the Philippines, passing over mostly poor central regions, while also bringing heavy rain to the densely-populated capital of Manila slightly to the north.