The agency said all the birds at the farm will be slaughtered and the premises disinfected, adding that veterinary services are conducting checks at neighboring farms.
It is the first time the virus has been detected among domestic poultry in the country.
The first bird flu case was reported in the Czech Republic in the spring of 2006, with 13 registered incidents since then. Last year, the H5N1 strain was detected among wild geese.
Russia's food safety watchdog Rosselkhoznadzor said it will impose a temporary ban on poultry imports and related products from the Czech Republic.
"This is standard procedure. The Czech authorities will be formally notified within the next two days," press secretary Alexei Alexeyenko said.
