The World Organisation for Animal Health (OIE) and the Food and Agriculture Organisation (FAO) reported an outbreak among poultry in northern Nigeria that had killed 40,000 birds.
The outbreak occurred on a large commercial battery-chicken farm in Jaji, Kaduna state, the world veterinary watchdog said on Wednesday.
"The OIE/FAO reference laboratory for avian influenza in Padova, Italy, has characterised the isolate as a highly pathogenic H5N1," it said.
"The OIE, together with the FAO, will take immediate action and coordinate a common response to this event. A team of experts will be sent to the affected area in order to assess the situation and provide technical advice to the national authorities."
The farm had 46,000 birds, comprising egg-laying chickens as well as ostriches and geese, before the outbreak occurred on 10 January.
A total of 42,000 birds had been infected, the OIE said, citing a notification from the Nigerian ministry of agriculture.
The Nigerian authorities said they had taken measures to tackle the outbreak through disinfection, quarantine and restrictions on animal movements, the OIE added.
"This is a worrying development, as we had been afraid that the continent could be affected"
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Jaji is a rural town in a farming district of northern Nigeria, 300km north of Abuja, on the main trading route from the capital through Kaduna and Zaria to Kano.
Maria Zampaglione, the OIE spokeswoman, said it was the first time H5N1 avian influenza had been detected in Africa.
Jean-Luc Angot, the agency's deputy director general, said: "This is a worrying development, as we had been afraid that the continent could be affected. It means that the disease has got a foothold on the continent."
The H5N1 bird flu virus erupted in Hong Kong in 1997, where it killed six people.
It surfaced again in Asia in 2003, circulating among poultry flocks in Southeast Asia, China and South Korea before spreading to the southeastern corner of Europe in October 2005, touching Balkan countries and Turkey.