More than 2.4 million people had fled in southern China's Guangdong province by Sunday evening, state media said.
Videos posted by residents showed the incredible power of the typhoon as it caused buildings to sway, sucked reams of documents out of the shattered office windows, tore down scaffolding and pushed walls of water into low-lying parts of the island.
The Thai Meteorological Department says that Mangkhut will weaken into a tropical storm as it moves into north Vietnam and will cause heavy rains and potentially high winds in northern and northern-eastern Thai provinces.
Numerous missing in the Philippines are gold miners and their families, feared buried in the landslide after seeking shelter in a bunkhouse-turned-chapel in the far-flung village of Ucab, in Itogon town, Benguet province. It shut casino gambling operations late on Saturday, authorities said, with China's People's Liberation Army on standby for any disaster relief assistance.
In Hong Kong, waters surged in the famous Victoria Harbour and coastal fishing villages, from which hundreds of residents were evacuated to storm shelters.
The storm made landfall in the Guangdong city of Taishan at 5pm, with wind speeds of 100 miles per hour.
A "super typhoon" swirled towards Hong Kong and the Chinese coast on Sunday, gaining in strength over the South China Sea after hurtling through the Philippines, where it wreaked devastation that killed at least seven.
A scene of damaged crops following the landfall of typhoon Mangkhut on September 15, 2018 in Alcala.
Hong Kong weather authorities issued their maximum alert for the storm, which hit the city with gusts of more than 230 kilometres per hour and left 213 people injured, according to government figures. All high-speed and some normal rail services in Guangdong and Hainan provinces were also halted, the China Railway Guangzhou Group Co said.
Residents stand by a flooded road following the onslaught of Typhoon Mangkhut in Tuguegarao city in Cagayan province.
Francis Tolentino, an adviser to Philippine President Rodrigo Duterte, said the 12 died mostly in landslides and houses that got pummeled by the storm's fierce winds and rain.
Police Superintendent Pelita Tacio said 34 villagers had died and 36 remained missing in the landslides in Ucab and another village in Itogon town.
The bunkhouse was a shelter at an old mining site in the town of Itogon, almost 200km north of Manila, which "went missing" during a landslide, said Itogon Mayor Victorio Palangdan. Hong Kong airline Cathay Pacific said all Sunday flights would be grounded.
Rescuers resumed their search efforts on Monday morning, using pikes and shovels to dig into the mud, with the use of heavy equipment limited on the soaked ground.
Farmers have scrambling to save their crops from Mangkhut - which struck at the beginning of harvesting season - while those in the typhoon's path who can not evacuate have been stocking up on supplies.
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