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 is still punching powerful winds and gusts equivalent to a category 4 Atlantic hurricane.
Thousands of people evacuated high-risk areas following major flooding and landslide warnings.
Authorities are taking extra precautions as they draw comparison with Typhoon Haiyan, which devastated central areas of the archipelago in 2013, and killed 6,300 people, many in storm surges that reached as high as eight metres.
But disaster officials said the country was now better prepared in terms of evacuating high-risk communities, which had experienced a super typhoon in 2016 and knew what was coming.
Presidential adviser Francis Tolentino said the 12 died mostly in landslides and in houses that were pummelled by the storm's fierce winds and rain.
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.
Earlier on Saturday, the storm left at least 16 dead in the Philippines earlier in the day as it lashed Luzon with sustained winds of over 105 miles per hour and gusts of almost 162 miles per hour and inundated the archipelago's northern island with floodwaters.
On Wednesday, President Rodrigo Duterte deployed some cabinet secretaries to areas that will most likely be hit by the typhoon to monitor the situations on the ground.
Hundreds of thousands of people could be left without food, shelter and water - this is going to put a real strain on everyone affected.
"Last time we had a super typhoon, there were 14,000-plus of totally destroyed houses and about 40,000-plus of partially destroyed houses", he told news channel ANC.
It is the start of the rice and corn harvesting season in Cagayan province, where farmers have been scrambling to save what they can of their crops.
Earlier Friday, the storm passed over the USA territory of Guam, knocking down trees and taking out 80 percent of the island's power.
A government damage assessment was underway except in areas still being battered by winds and rain.
"I'm so anxious also nervous because of course they are our church members as well as our relatives, our families are there because according to them this is one of the strongest typhoon that visited the Ilocos Norte", Corpuz said.
After passing the Philippines the island of Taiwan could receive strong storm force winds and heavy rains, following which it will be Hong Kong and mainland China that is on watch for future impacts.
As shown from the Himawari 8 satellite, Typhoon Mangkhut heads towards Hong Kong.
Hong Kong officials have called on residents to prepare for the worst and are urging them to stay indoors.
The most ferocious typhoon to hit the disaster-prone Philippines this year slammed ashore before dawn on Saturday in Cagayan province on the northeast tip of Luzon island.
Known locally as Ompong, Typhoon Mangkhut at one point had maximum gusts of 305 kph (190 mph) before it left the Philippines and moved towards Hong Kong and southern China, with wind speeds that reduced to 170 kph (106 mph) then to 160 kph in the evening.