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Ministry spokesman Andrei Alyabyev said: "Suspicions containers with pipes were found in two other shops, they are being defused."
Russian media reported the containers had been set up with timing mechanisms to go off as time-bombs.
The attack on the stores, belonging to the Maksidom chain, is believed to be the work of criminals rather than terrorists.
Local media quoted prosecutors as saying the gas was methyl mercaptan, a compound added to domestic gas to give it its odour.