Tens of thousands of passengers were stranded in the city's global airport on Sunday, the airport authority said, with airlines including the city's flagship carrier, Cathay Pacific, having already cancelled many flights.
Macau has been cautious this time, with officials saying its hut casino gambling operations late on Saturday and China's People's Liberation Army on standby for any disaster relief assistance.
Thousands of people evacuated high-risk areas following major flooding and landslide warnings.
Hong Kong authorities lifted the storm alert to its highest level on Sunday as typhoon Mangkhut was fast approaching, bringing the city to a standstill as residents prepared for the threat of heavy rain, storm surges and flooding.
The South China Morning Post on Wednesday reported that the system could turn out to be stronger than any of the 15 typhoons that have been given Hong Kong's highest warning signal and looked set to be one of the strongest to ever hit Southeast Asia.
Mangkhut is already the storm of 2018, and is now packing sustained winds of 165 km, with gusts up to 205 km per hour.
According to CNN, the typhoon's winds reached 180 miles per hour at one point.
Mangkhut is due to make landfall in Guangdong later Sunday. Power to some areas could also be reduced as a precaution, say grid operators.
Francis Tolentino, political adviser to President Duterte, told the BBC there was also extensive crop damage in the agricultural heartland state.
Nearly all buildings in the city of Tuguegarao, Cagayan's provincial capital, sustained damage, a government official said.
The storm, which packs a 900km rain band and strong winds, is heading towards southern China.
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In nearby Fujian province on the Chinese mainland, 51,000 people were evacuated from fishing boats and around 11,000 vessels returned to port on Saturday morning.
Typhoon Mangkhut has ripped through the Philippines, causing swift damage and at least 12 deaths.
Vehicles move through flooded roads as strong winds blow at Roxas Boulevard in Manila, Philippines, September 15, 2018 in this still image taken from video obtained from social media.
"This was the strongest and the worst storm that I've ever experienced in my life", Teresita Antonio, 54, told The New York Times in Claveria, a corn- and rice-growing area on Luzon's northern coast.
Because communications and electricity were knocked out across much of the region where about five million people were in the typhoon's direct path, officials are still assessing the human and material cost.
A resident from Yangjiang said she was concerned about the looming storm and had stocked up on food supplies.
The Philippine budget airline Cebu Pacific, along with multiple Hong Kong airlines including Cathay Pacific, also announced flight changes.
"Because Mangkhut will bring winds and rains of extraordinary speeds, scope and severity, our preparation and response efforts will be greater than in the past", Lee said.
Almost 37 million people are estimated to be in the storm's path, according to the Global Disaster Alert and Coordination System.
Typhoon Haiyan left more than 7,300 people dead or missing and displaced over 5 million in the central Philippines in 2013.
Most shops and public services are shut, and more than 800 flights have been cancelled at Hong Kong International Airport - affecting more than 100,000 passengers.