By Agence France-Presse
The massive storm cut a swathe of destruction when it struck the northern tip of Luzon island, threatening the lives and homes of roughly four million people.
"As we go forward, this number will go higher," Ricardo Jalad, head of the national civil defence office, told reporters, referring to the death toll.
As the powerful storm left the Southeast Asian archipelago and barrelled towards densely populated Hong Kong and southern China, search teams in the Philippines began surveying the provinces that suffered a direct hit.
"We believe there has been a lot of damage," said Social Welfare Secretary Virginia Orogo as thousands of evacuees took refuge in emergency shelters.
Mangkhut was packing sustained winds of 170 kilometres (105 miles) per hour and gusts of up to 260 km per hour as it left the Philippines.
An average of 20 typhoons and storms lash the Philippines each year, killing hundreds of people and leaving millions in near-perpetual poverty.
Thousands of people fled their homes in high-risk areas ahead of the storm's arrival because of major flooding and landslide risks.
In Taiwan, a woman was swept away by high waves caused by the typhoon, the government said.
The two lifeless bodies of the two women in the Philippines were pulled from the soil of a hillside that collapsed after the storm's torrential rains, police said.
- 'We are terrified' -
Residents had started lashing down their roofs and gathering supplies days before the arrival of the storm.
"Among all the typhoons this year, this one (Mangkhut) is the strongest," Japan Meteorological Agency forecaster Hiroshi Ishihara told AFP on Friday.
"This is a violent typhoon. It has the strongest sustained wind (among the typhoons of this year)."
After blasting the Philippines, Mangkhut is predicted to hurtle towards China's heavily populated southern coast this weekend.
"They (authorities) said this typhoon is twice as strong as the last typhoon, that's why we are terrified," Myrna Parallag, 53, told AFP after fleeing her home in the northern Philippines.
"We learned our lesson last time. The water reached our roof," she said, referring to when her family rode out a typhoon at home in 2016.
The country's deadliest on record is Super Typhoon Haiyan, which left more than 7,350 people dead or missing across the central Philippines in November 2013.
Poor communities reliant on fishing are some of the most vulnerable to fierce typhoon winds and the storm surges that pound the coast.
"The rains will be strong and the winds are no joke... We may have a storm surge that could reach four storeys high," Michael Conag, a spokesman for local civil defence authorities, told AFP.
As the storm heads for China's southern coast, Cathay Pacific airline said it expects more than 400 flight cancellations over the next three days.
The Hong Kong government said Mangkhut will pose "a severe threat to the region" as many residents in the city and neighbouring Macau stocked up on food and supplies.
The president of neighbouring Taiwan, Tsai Ing-wen, told citizens to be ready.
"The typhoon is powerful and even it's not expected to make a landfall in Taiwan, we should be well prepared and not... take it lightly," she wrote on Facebook.