A 36-year-old Indonesian domestic helper with a history of travelling to the mainland city of Shenzhen and coming into contact with live poultry has been infected and is in critical condition, Health Secretary Ko Wing-man said, according to the broadcaster RTHK.
The patient was admitted to hospital on November 27 after developing a cough and shortness of breath. She was transferred to intensive care at the city's Queen Mary Hospital last Friday, the report added.
In April Taiwan reported its first case, a 53-year-old man who had been working in eastern China.
The man was eventually discharged but the case prompted the island's authorities to begin research into a vaccine they hope to roll out by late 2014.
Secretary Ko said Hong Kong had suspended the import of live poultry from Shenzhen and escalated the grade of its flu contingency plan to "serious", according to the RTHK report.
People who had come into close contact with the patient recently have also been admitted to another hospital for isolation and testing.
The infection comes 10 years after the Severe Acute Respiratory Syndrome (SARS) outbreak swept through Hong Kong, killing 299 people and infecting around 1,800.
Avian flu viruses have been around for a very long time in wild birds. They do not generally cause disease in humans, though in rare cases they mutate and jump species.
A report by researchers published in The Lancet medical journal in October said closing live poultry markets, though a huge economic setback, is a sure-fire way of curbing H7N9.