Junaidu Maina, agriculture director for the livestock department, said the infected chickens and ducks were located last week in the northern cities of Kano and Katsina.
"Immediate actions have already been taken to control the outbreak. The affected farms are being depopulated and disinfected," he said.
The virus, which can spread to humans, was first discovered in Nigeria in February 2006 and infected poultry in 25 states before being contained. The last Nigerian outbreak was in October 2007.
The outbreak of highly pathogenic H5N1 avian flu began in Asia five years ago and has been found in about 60 countries and territories, according to the World Organisation for Animal Health. The virus has killed 243 people since 2003.
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