The city imposed a 21-day alert and shutdown of poultry imports from mainland China.
Ever since the last bird-flu outbreak in Hong Kong in 2002, the city has used the H5N2 vaccine, while mainland China, where outbreaks are more frequent, vaccinates against the more virulent H5N1 strain that has a mortality rate of nearly 100 percent.
"This virus has mutated slightly over the last six years, and because of that we have asked the University of Hong Kong to do research to find out if there is a need to replace the H5N2 with the H5N1 vaccine," says York Chow, Hong Kong's secretary of food and health.
Scientists for years have feared the H5N1 strain could mutate into a form more easily transmissible to humans, resulting in a world pandemic.
The current Hong Kong outbreak is on a farm in the city's semi-rural New Territories region that borders the mainland. The birds found dead carried the H5N1 strain.
Meanwhile, Indonesia's Ministry of Health confirmed two new human cases of H5N1 bird flu last month. One, a 9-year-old girl, recovered after 20 days, but a 2-year-old girl died.