The outbreak, previously confined to five remote areas of Siberia, has struck a major industrial region - Chelyabinsk in the Ural mountains, which separate Asia from Europe.
"All ill and infected birds are being slaughtered there," the Agriculture Ministry said on Monday in a statement.
It was unknown whether the virus found in Chelyabinsk was the deadly H5N1 strain that has killed more than 50 people in Asia since 2003 and has hit Russian Siberia as well as Kazakhstan and Mongolia since mid-July.
Carried by flocks of wild birds migrating from Siberia to warmer regions, the virus has been steadily moving westwards through the regions of Novosibirsk, Tyumen, Omsk, Kurgan and Altai.
Chelyabinsk, separated from European Russia by the Ural mountains and technically still in Siberia, is the westernmost region to have been struck.
It is about 1000km from the region where the first flu outbreak was reported.
"All ill and infected birds are being slaughtered there"
Agriculture Ministry statement
Although no humans have been affected, there are fears the disease could spread to humans on the Eurasian landmass, possibly unleashing a global influenza pandemic.
Media reported that roads leading to the infected village of Oktyabrskoye in Chelyabinsk had been cordoned off to prevent the virus from spreading.
In other affected regions, police boosted road checks, and 400 domestic birds were culled in Chelyabinsk to block the virus that has killed more than 10,000 birds countrywide.
Officials said wild birds, increasingly active in August as they prepare to migrate ahead of winter, were to blame.
"Results of epizootic checks have shown that they (migrant birds) are the main source of infection," Ria-Novosti news agency quoted an official with the Novosibirsk state consumer rights watchdog as saying.
There was no word on Monday on the situation in Kazakhstan and Mongolia where bird flu has been registered along their sprawling borders with Russian Siberia.