The spokesman said that bomb disposal experts had disabled the device, equivalent to 9-12 kg (20-27 lbs) of TNT, using a controlled explosion.
Sporadic terrorist attacks and militant clashes remain rather common in Russia's republics of Ingushetia and Daghestan, as violence spills over from neighboring Chechnya, although the Kremlin has ended its campaign to fight separatists and terrorists there.
In mid-June one person was killed in a bomb blast near the central marketplace in downtown Makhachkala.
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The clash of Russian and Western interests has given rise to a geopolitical battle. German politicians are trying to leave all doors and windows open for dialogue with Russia. Moscow does acknowledge this, and Germany is probably the only country with which it is ready to discuss European security.