The virus was found in wild swans and ducks in two regions bordering the Black Sea and the Caspian Sea, the ministry said. This region is located east of Ukraine's Crimea, where officials have been trying to contain the spread of the disease since early December 2005.
"Cold weather forces wild fowl to migrate over short distances, spreading the (bird) flu virus of group A, H5N1 strain," the ministry said in a statement. "Recently, the virus has been found in wild swans and wild ducks in the littoral zone of the Krasnodar region and Dagestan."
The ministry's animal and plants health inspector, Rosselkhoznadzor, has sent veterinary experts to the region to monitor the situation.
Russia has been battling with bird flu in poultry since July, culling more than 600,000 domestic fowl.
No new cases of the virus have been found in Russia since the end of last year, but veterinaries warned migratory birds could bring the virus back in the spring.