Over a million birds were slaughtered last year
The farms - in the Kam Tin area of the New Territories - were found to be infected with the H5-type virus, which officials fear could spread to humans.
Hong Kong has already killed more than 300,000 young birds in the past few months, and has placed dozens of poultry farms under quarantine to prevent the disease spreading.
The measures were taken after scientists warned the virus could mutate in a similar way to one which killed six people in 1997.
But the Agriculture, Fisheries and Conservation Department said the disease had been contained.
"There is no sign to show that this is a new outbreak of disease or that the disease is spreading to farms outside the quarantine area," a statement said.
"As the newly confirmed infected farms have been put under quarantine from 5 February, no chickens have left these farms since then," it added.
Popular food
The authorities have also ordered the closure of poultry markets for two days per month for disinfecting.
Chicken is a popular food in Hong Kong - residents consume an average of 100,000 birds a day.
But a deadly version of the bird flu virus crossed the species barrier in 1997 to kill six people. Over a million birds were slaughtered as a result.
And last May, another outbreak flu led to the slaughter of Hong Kong's entire poultry population - 1.37 million birds including geese, ducks and quail - though the strain was found to be non-fatal to humans.