He said officials were still awaiting results on tests taken in a third suburban district, Podolsk, where 44 birds were reported to have died on Saturday.
Russian television broadcast footage showing veterinary workers clad in protective suits checking homes in one district and spraying vehicle tyres with disinfectant, while police began enforcing quarantine in an effort to prevent spreading of the virus.
Regulators also shut down an outdoor poultry market in Moscow on Saturday where some of the dead birds appeared to have been bought.
Russia had its first reported cases of the H5N1 strain in Siberia in 2005, and outbreaks have since occurred farther west, but mostly in southern areas distant from the capital.
No human cases of bird flu have been reported in Russia.
Bird flu cases were registered in 93 towns or settlements in Siberia and southern Russia last year, according to the RIA-Novosti news agency. The country's first outbreak this year was registered last month in the Krasnodar territory, an agricultural region near the Black Sea.
Since it began ravaging Asian poultry farms in late 2003, the H5N1 strain has killed at least 167 people worldwide, according to the World Health Organisation.