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There were reports of 34 people injured in Hong Kong while in the city of Macau, across the Pearl River estuary, three people were killed, authorities there said.
In Hong Kong, more than 450 flights were cancelled, financial markets suspended and schools closed as Hato bore down, the first category 10 storm to hit the city since 2012.
"I've never seen one like this," Garrett Quigley, a longtime resident of Lantau island to the west of the city, said of the storm.
"Cars are half submerged and roads are impassable with flooding and huge trees down. It's crazy."
Many skyscrapers in the heart of Hong Kong were empty and dark as office workers stayed at home.
Hato churned up Hong Kong's Victoria Harbour and triggered large swells and big waves on some of the city's most popular beaches, with serious flooding in low-lying areas.
In residential districts like Heng Fa Chuen on densely populated Hong Kong island, waves smashed against the sides of oceanfront buildings and surged over a promenade, swamping roads and vehicles parked nearby.
Construction cranes swayed at the tops of skyscrapers, windows imploded and nearly 200 trees were uprooted, while some people used canoes to venture out into flooded streets.
Authorities downgraded the storm to a category eight by mid-afternoon.
The storm also caused a power blackout across most of the gambling hub of Macau for about two hours, residents said, with disruption to mobile phone and internet networks.
The former Portuguese colony's casinos, however, had backup power, two casino executives told Reuters.
The storm also made landfall in China's Guangdong province, in Zhuhai city adjacent to Macau, China's Xinhua state news agency.
Numerous flights and trains were cancelled in Guangdong province, with Shenzhen's International Airport particularly badly hit.
Thousands of residents along the Chinese coast were evacuated and fishing vessels were called back to port.
Maximum winds near Hato's centre were recorded at a destructive 155 kph (95 mph).
A senior scientific officer for the Hong Kong observatory warned that sea levels could rise several metres in some places, with the government issuing flood alerts and opening 27 shelters across the city.
Trading in Hong Kong's financial markets was halted for the day, the stock exchange said. Typhoon Nida in August last year was the last storm to close the exchange for the whole day.
The city's flagship carrier, Cathay Pacific, and Hong Kong Airlines said the majority of their flights to and from Hong Kong between 2200 GMT Tuesday and 0900 GMT Wednesday would be cancelled.
Other transport services, including ferries to the gaming hub of Macau and outlying islands in Hong Kong, were suspended.