The carcass was found to have a "highly pathogenic H5N1 avian influenza virus," York Chow, Hong Kong's secretary for food and health, said in a statement announcing the cull.
Hong Kong has raised the territory's bird flu alert to "serious," and increased monitoring for influenza cases at hospitals, The New York Times reported Wednesday.
The sale and import of live poultry will be suspended for 21 days, Chow said, while officials attempt to determine if the carcass was imported or obtained from a local source.
"I understand that it will cause inconvenience to the public, and the poultry trade will also encounter losses," Chow said. "However, to safeguard public health, we need to adopt decisive and effective measures to prevent and control the spread of the virus."
Hong Kong was the site of the world's first major outbreak of avian flu among humans. Six people died in 1997.