The 65-year-old man was the second person to die from the virus in Hong Kong, and the third reported case of H7N9 infection.
"The patient passed away at 7:02pm tonight," a government statement released late today said.
Initial investigations showed that the man had travelled to the neighbouring mainland Chinese city of Shenzhen a week before he was infected.
He had not been directly exposed to live poultry, but had probably contracted the virus outside the city, Hong Kong Centre for Health Protection controller, Leung Ting-hung, had told reporters last week.
Five close contacts of the man remain under quarantine, with 98 other contacts, including healthcare workers and others, under medical surveillance.
An 80-year-old man died on Boxing Day last year after he was infected with H7N9, Hong Kong's first death from the virus.
The case was the second reported incidence of H7N9 infection in the city after a 36-year-old Indonesian domestic helper was diagnosed in early December.
The H7N9 outbreak began in China in February 2013 and reignited fears that a virus could mutate to become easily transmissible, potentially triggering a pandemic.
As of January 12, a total of 169 human cases of avian influenza H7N9 have been confirmed on the mainland.
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