"We feel that Hong Kong is facing a new alert for bird flu," said York Chow, secretary for food and health.
Chow said the chickens, found Monday at a farm with 60,000 birds, had the H5 virus and further tests were being done to see if they had the deadly H5N1 strain.
The farm and neighboring poultry operations were declared part of an infected zone, and about 80,000 birds in the area would be killed to prevent the spread of the disease, Chow said.
He added that the 21-day ban on poultry imports would last through the Christmas holiday, a time when chicken is an important dish in celebratory dinners.
Hong Kong's biggest bird flu outbreak was in 1997, when the H5N1 strain jumped to humans and killed six people. That prompted the government to slaughter all 1.5 million poultry in the territory.
In 2001, the government also carried out a massive poultry slaughter, killing 306,000 birds in wholesale and retail markets and 951,000 in local farms to eradicate an outbreak of bird flu. The city now has 600,000 birds, Chow said.
At least 245 people have died of bird flu worldwide since 2003, according to the World Health Organization.
Hong Kong's government has been encouraging retailers to stop selling live birds, and the majority of shops have given up their licenses to sell live poultry. But eating fresh chicken is an important part of the culture and many shoppers still want freshly slaughtered birds.