Deadly H7N9 virus was discovered in poultry imported from mainland China, after which Hong Kong authorities said on Wednesday that they will cull 15,000 chickens.
The announcement came days after a woman was diagnosed with the virus, prompting the city to raise its alert level for avian influenza.
"The department will take measures to destroy a total of 15,000 number of live chickens at the Cheung Sha Wan market starting this morning," the city's health minister Ko Wing-man told reporters at a press conference early Wednesday.
Imports from the mainland have also been suspended, he said.
The virus was discovered through a "rapid testing" system, introduced to check birds for the disease, in a sample of 120 chickens imported from the nearby Chinese city of Huizhou, Ko said.
The tests were done after a larger batch of chickens from the same area tested positive for the H7 strain of the virus.
"The rapid testing showed... that this batch of chicken carries the H7N9 virus," Ko said.
A 68-year-old woman was hospitalized last Thursday after returning to Hong Kong from the southern Chinese city of Shenzhen almost two weeks earlier, although it has not been confirmed where or how she contracted the virus.
Ten people had previously been diagnosed with H7N9 in Hong Kong, including three who died. All had contracted the virus in mainland China, according to Hong Kong's Centre for Health Protection.
The outbreak, which first emerged on the mainland in February 2013, has reignited fears that a bird flu virus could mutate to become easily transmissible between people, threatening to trigger a pandemic.
In response to the new case -- the city's first since early 2014 -- Hong Kong announced it was raising its response level in hospitals to "serious" from "alert", with extra precautions implemented from Sunday.
Hong Kong slaughtered 20,000 chickens in January after the virus was found in poultry imported from the southern Chinese province of Guangdong.
A four-month ban on live poultry imports from mainland China was then imposed to guard against the disease.
Hong Kong is particularly alert to the spread of viruses after an outbreak of Severe Acute Respiratory Syndrome swept through the city in 2003, killing 299 people and infecting around 1,800.
There have been 469 cases of H7N9 in mainland China since 2013, according to Hong Kong's CHP.