The storm made landfall before dawn in Cagayan province on the northern tip of Luzon island, with gusts of up 255km (160 miles) per hour.
More than 5 million people were at risk from the storm, which the Hawaii-based Joint Typhoon Warning Center downgraded from a super typhoon but one that's still punching powerful winds and gusts equivalent to a category 4 Atlantic hurricane.
Gov. Bojie Dy reports more than 5,000 people have been evacuated from coastal areas in Isabela province.
Philippine authorities have said they are better prepared than in 2013, when Typhoon Haiyan devastated central areas of the country and killed 6,300 people.
Manila: Super typhoon Mangkhut is expected to threaten China's Guangdong coastline, possibly including Hong Kong, with a direct strike in a few days that may cause as much as $US120 billion ($139 billion) in damage and economic losses.
Super Typhoon Mangkhut - the biggest storm of the year - smashed through the Philippines on Saturday, claiming its first victims as two women were killed when a rain-drench hillside collapsed on them and another drowned in Taiwan.
Airlines across the region cancelled more than 100 flights on Saturday as Super Typhoon Mangkhut slammed into the Philippines and was set to disrupt travel from Hong Kong to Japan. There have been no reports of casualties so far, said Harry Roque, President Rodrigo Duterte's spokesman.
"Almost all of the buildings here have been damaged, the roofs were blown away", Rogelio Sending, a government official in Tuguegarao, the capital of Cagayan, told Reuters.
Thousands of people have fled from the path of Typhoon Mangkhut (local name Ompong) which picked up strength as it barreled toward the Philippines' Cagayan region on Friday.
"We're praying that there will be less damage this time, although we know that this one will be very strong", Banez said.
In Legazpi city in Albay province, evacuee Delaila Pasion said: "During the previous monsoon rains, half of our house was destroyed so I wanted to take my grandchildren to safety so they would not get hurt".
"The rains will be strong and the winds are no joke".
Earlier Friday, the storm passed over the US territory of Guam, knocking down trees and taking out 80 percent of the island's power.
Super Typhoon Mangkhut is hurtling through the Pacific toward Asia boasting winds as fast as 180 miles per hour.
Mangkhut led Taiwan to announce a series of rain, wind, and wave warnings on September 15, and the typhoon is expected to hit China between Hong Kong and Hainan late tomorrow afternoon.
The Philippines Red Cross said it had activated 30,000 volunteers across Luzon to prepare for the impact of the storm and dispatched a "humanitarian caravan" consisting of rescue and relief vehicles to the parts of the island expected to be among the worst affected.
The typhoon is now moving west towards China.
The observatory warned of rough seas and frequent heavy squalls, urging residents of the densely populated financial hub to "take suitable precautions and pay close attention to the latest information" on the storm.
Other grounded flights include AY 102, which is due to leave Honk Kong for Helsinki on Sunday, and AY 5831 which is to fly passengers from Hong Kong to Helsinki via Bangkok also on Sunday, the airline's communications department said.
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