Fears over avian flu have grown following the deaths of two men from the H7N9 strain in Hong Kong since December. Both had recently returned from mainland China.
The number of human cases in China this month is 102 with 22 deaths, according to an AFP tally, and the worst-hit province of Zhejiang has closed live poultry markets in major cities there.
Officials wearing masks and protective suits piled dead chickens into black plastic bags at Hong Kong's Cheung Sha Wan market today, where the virus was found, television footage showed.
Vendors are unable to buy live chickens and farmers have nowhere to send their stock, leaving traders and shoppers disappointed in the holiday period.
Traditionally Hong Kongers buy a live chicken for Lunar New Year celebrations with family.
"I wanted to buy one for my mother for the festival," one shopper in the city's bustling Wan Chai Road food market told AFP.
"But now there is none, I will have to buy something else. Live chickens just taste better than frozen chickens. The texture is different," said the woman, who gave her name as Monica.
"Of course there is inconvenience because we still need to pay the rent and we want to get paid. The sales volume will be affected", a 59-year-old trader who gave his surname as Law told AFP.
The mass cull started at 10:00 am, local time and was set to last for 10 hours, the agriculture department spokesman said.
Chickens would be given a "chemical treatment" to kill them, after which they would be sent to a landfill, he added.
The move comes days after Hong Kong introduced widespread testing of imported live poultry following growing public concern over the safety of imports, particularly from the mainland.
"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 today.
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