Hong Kong will cull approximately 20,000 chickens after discovering the H7N9 avian influenza virus in a batch of poultry imported from mainland China, authorities said Monday.

The positive reading came just days after the southern Chinese city introduced widespread testing of imported live poultry following growing public concern over the safety of imports, particularly from the mainland.

Two people have died from the human form of the virus in Hong Kong since the first infection was publicly reported in December.

On Friday the city introduced a serological test for H7 avian influenza in live poultry and soon discovered a batch that tested positive for the virus.

"A government department has confirmed that the sample chicken from the chicken imported from the mainland tested positive for H7N9 avian influenza virus," Hong Kong health minister Ko Wing-man told reporters late Monday.

"All the poultry in the wholesale market will be destroyed tomorrow morning... the total number of chickens concerned amounts to 20,000," Ko said, declaring the market to be an "infected place".

The government's decision comes less than a week before Chinese New Year, which starts on Friday, when live chicken is a popular dish at banquets and family gatherings.

"Because we have to close the wholesale poultry market... for the next 21 days, there will be no supply of live chicken," Ko said, suggesting that residents eat frozen chicken instead.

The market in the Cheung Sha Wan region of the city, which holds imported poultry into the city until cleared of infection, will be closed for disinfection.

Hong Kong culled 17,000 chickens in December of 2011 and suspended live poultry imports for 21 days after three birds tested positive for the deadly H5N1 strain of bird flu virus.

A 65-year-old Hong Kong man with H7N9 died on January 14, less than a week after he was infected with the deadly virus. He was found to have traveled to the neighbouring mainland Chinese city of Shenzhen a week before he was infected.

An 80-year old man died on Boxing Day last year after he was infected with the virus.

Hong Kong is particularly alert to the spread of viruses after an outbreak of Severe Acute Respiratory Syndrome (SARS) swept through the city in 2003, killing 299 people and infecting around 1,800.

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.