The head of Russia's National Anti-Terrorist Committee said the blast hit a train between Sennaya Ploshchad and Tekhnologichesky Institut stations.
The committee said an explosive device was later found and made safe at another station nearby.
Prime Minister Dmitry Medvedev said in a Facebook post that the explosion was a "terrorist attack".
An anti-terror investigation has been opened, but other possible causes are being investigated.
The Russian authorities are sensibly being cautious before apportioning blame for Monday's metro blast. An earlier quote by the prosecutor-general that it was an act of terrorism was quickly retracted.The FSB security service, the successors to the Soviet-era KGB, have skilled investigators, including forensic explosive experts. They will have been examining security camera footage and the explosive residue for clues, as well as the second device that was found intact and defused.
Their suspicions are likely to focus on two possible suspects, neither yet confirmed. First, an IS-inspired group enraged by recent Russian airstrikes in Syria. And second, Chechen nationalists (or even a combination of both).
Chechen militants and international jihadists do have a track record of plotting to attack Russia's transport hubs, notably in Moscow. An estimated 7,000 Russians have traveled to Syria to join extremist groups - and some have returned.
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