The deadly H5N1 virus was found at a poultry farm, the first outbreak on a Hong Kong farm here in nearly six years.
"We have identified the virus as H5N1 this afternoon following a series of tests," a spokeswoman for the Agriculture, Fisheries and Conservation Department told AFP.
The government announced Tuesday that bird flu was found at the farm near the border with China, and ordered the slaughter of more than 90,000 chickens by end of this week.
Initial tests revealed the H5 virus and the results of follow-up tests announced Thursday identified it as the H5N1 strain. Authorities said they have not found any positive sample from the other farms they have tested so far.
The World Health Organization said Thursday it would monitor the outbreak.
"We are watching it very carefully," Peter Cordingley, a spokesman for WHO's Western Pacific regional office, told AFP.
Cordingley said they were not surprised by the outbreak because the virus is very versatile and tended to be more active in winter.
The origin of the outbreak remains unclear. The government on Wednesday said it had commissioned scientists to find out if the vaccine they have been using since 2003 to protect chickens against bird flu remains effective, after acknowledging the virus has "changed slightly".
Some experts have criticised the government for not having considered the problem of mutation earlier, Chinese newspapers reported Thursday.
Meanwhile, Hong Kong Poultry Wholesalers Association said that the outbreak could be linked to the illegal smuggling of fertilised eggs from China containing infected chicken embryos.
"There is a very big connection between the outbreak and smuggled fertilised eggs," Tsui Mingtuen, the association chairman, told AFP following a meeting with his members Thursday.
Tsui claimed he had evidence and witnesses to support his allegation.
York Chow, the city's Secretary for Food and Health, said they had not detected any smuggling of fertilised eggs but that it could be a possible reason for the outbreak.
"I think theoretically this can happen, but we do not have any evidence so far. I would appeal to the trade to give us any evidence if they can actually provide information," Chow said in a statement issued Thursday.
Wong Yeechuen, owner of the farm where the outbreak occurred, denied having smuggled any fertilised eggs from China and asked the association for evidence to substantiate its allegation.
"The allegation is ridiculous," he told Cable TV.
"There is no chance for a chicken to survive after hatching from infected embryos. If their allegation is true, how come some of the infected chickens in my farm were as old as 40 to 50 days?" he said.
Hong Kong was the scene of the world's first reported major H5N1 bird flu outbreak among humans in 1997, when six people died.
The last outbreak in a poultry farm took place in 2003, since when the government has required farmers to vaccinate their birds against the flu.
The deadly virus has killed about 250 people worldwide since late 2003.