Nigeria, Egypt and Niger have already reported cases in poultry flocks. Confirmation of the infection came from the Pasteur Institute in Paris following tests on samples taken from ducks in Maroua.
"Yesterday, we received confirmation from Paris that one of the samples was positive, that a case of H5N1 was effectively detected in one of the ducks," Cameroon Livestock Minister Sarki Aboubakary told Reuters.
Cameroon's Far North province borders Nigeria, where Africa's first H5N1 bird flu outbreak was confirmed on February 8.
No human cases have been discovered in Africa so far, but several Nigerians have been tested.
Precautions in place
Mr Aboubakary said health authorities had slaughtered all the remaining ducks on the Maroua farm.
They have also closed down all poultry markets in the region and put the country's veterinary services on a state of high alert.
Tests were being carried out on poultry in other farms in Far North province, and the government was preparing to vaccinate poultry if necessary, he added.
As the disease spreads in Africa, international experts are concerned that the world's poorest continent may not cope.
Africa is already battling HIV/AIDS and malaria and there are fears it lacks expertise and resources to combat this new health threat.
Cameroon has already banned all imports of poultry and poultry products from its neighbour.
Governments admit that regional borders are long and porous and it is impossible to control thriving local trade.
It is often carried out by merchants traveling on foot, by bicycle or motorbike along isolated bush trails and remote crossing points.
Gabon on alert
Suspected outbreaks in Gabon which borders Cameroon, Ethiopia, Gambia and Sierra Leone are also being investigated.
Gabon's authorities said they were tightening control and surveillance following confirmation of the outbreak in Cameroon.
Bird flu has killed at least 97 people in Asia and the Middle East since 2003. Humans contract the virus only through close contact with infected poultry.
Health officials are concerned that the spread of H5N1 in birds across Africa, where millions live in close contact with poultry in their homes and backyards, will increase the possibility the virus will mutate to become transmissible between humans.
Wealthy nations pledged almost US$2 billion to tackle bird flu at a donor meeting in Beijing in January and World Health Organisation officials say Africa will receive a sizeable portion of this to strengthen surveillance and other measures.
In most of Africa, the inability to detect avian flu quickly in animals or humans is delaying control measures.