Tass reported that over 20,000 people had been affected by the evacuation in Moscow alone.
"People were evacuated at 30 sites, in total more than 20,000 people were taken outside, this number is still being specified", an emergency services official told Russian news agency TASS.
Terrorists have earlier rocked Moscow on two occasions.
"There's never been anything like this before, it's 100 percent organized telephone terrorism", Frants Klintsevich, deputy head of the Defense Committee in the upper house of parliament, said in a telephone interview. Three more Siberian cities evacuated shopping malls, government offices, schools and hospitals. Sheremetyevo airport, the capital's busiest, tightened security after a threat, Interfax reported. Kremlin spokesman Dmitry Peskov referred questions on the issue to the security services. Several sources later reported police cordons had been lifted.
Largely, bomb threat calls were about Moscow's major shopping malls and Russian capital's three largest train stations - Leningradsky, Kazansky and Kievsky.
Sniffers dogs are searching the areas to confirm if there is any truth to the threats made. Initial reports indicated the evacuations might have been some kind of exercise. "Police dogs will be used to track down the bombs", the official said.Police said that most calls had come almost simultaneously and were still coming in."It seems like telephone terrorism and nothing else, but all the calls should be checked up", TASS quoted an official saying.