"The veterinary services have cordoned off the affected areas" in the commercial capital Cotonou and in Adjarra, a statement from the ministry said. The agriculture ministry said that vets had culled and incinerated more than 240 chickens during their disinfection of the two sites, both located in the southern coastal tip of the country.
"Samples were taken so that analyses could be carried out by an internationally renowned laboratory to either confirm or rule out the presence of the H5N1 bird flu virus," the statement said.
Several countries in Benin's immediate vicinity have been hit by the virus with one person having died from bird flu in neighbouring Nigeria.
Another neighbour, Togo, reported cases of H5N1 in poultry in June. Togo on Friday said it was banning imports of live poultry and poultry products from Benin.
Ghana, Togo's much larger neighbour, reported H5N1 in poultry earlier this year but the authorities have since declared the country clear.
Benin launched a bird flu prevention programme in February 2005. Two months later it banned imports of live poultry and poultry products from countries affected by bird flu and stepped up controls on imports from other countries.