Hong Kong began a mass cull of 20,000 chickens on Tuesday after the deadly H7N9 bird flu virus was discovered in poultry imported from mainland China, authorities said.

Fears over avian bird flu have grown following the deaths of two men in Hong Kong since December. Both had recently returned from mainland China.

Officials wearing masks and protective suits piled dead chickens into black plastic bags at the wholesale market in Hong Kong where the virus was discovered Monday, television footage showed.

"It (the culling) has started. It begun at around 10am," an Agriculture, Fisheries and Conservation Department spokesman told AFP.

The chickens would be given a "chemical treatment" to kill them, after which they would be sent to landfill, the spokesman said. The culling operation is set to last for 10 hours.

The positive H7N9 reading was discovered in chickens at Cheung Sha Wan market on Monday, which will be closed for 21 days for disinfection.

Cheung Sha Wan is the only wholesale poultry market in Hong Kong and is a holding centre for chickens awaiting test results.

Chicken supply to markets from local Hong Kong farms was also suspended.

The discovery of the virus came just days after Hong Kong introduced widespread testing of imported live poultry following growing public concern over the safety of imports, particularly from the mainland.

Hong Kong leader Leung Chun-ying, called into question the tradition of buying live chickens for fresher meat on Tuesday.

"In the long run, should we keep the customs of eating live chickens? Hong Kong people should look into this issue," he told reporters.

Buying live chickens is particularly popular ahead of Lunar New Year, which will take place on Friday, as they are cooked as part of celebratory meals.

Leung advised the public to be vigilant and "pay heed" to government guidelines on personal hygiene.

Local chicken farmers and wholesalers questioned why chicken imports suspected to contain viruses had not been detained at border check points.

"The government should be held fully responsible. It should have stopped the chickens at the border until they were confirmed to be clear of bird flu," wholesaler Cheng Chin-keung told the South China Morning Post Tuesday.

"Now the chickens from China get mixed with local chickens in the wholesale market and all of them have to be culled."

He said he would lose HK$5 million ($650,000).

A government spokesman told AFP that the chickens were sent to Cheung Sha Wan rather than being held at the border because there were no facilities for detaining them.

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.

A 65-year-old Hong Kong man with H7N9 died on January 14, after visiting the neighbouring mainland Chinese city of Shenzhen. 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 city 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.