In a dramatic move, diggers began to level the targeted buildings at around midnight, some of which housed food stores, pharmacies, florists and cafes next to busy metro stations.
The city authorities said the 97 buildings destroyed overnight -- some several storeys high -- were all built without proper authorisation, often in the 1990s soon after the breakup of the Soviet Union, and were dangerous.
Many Muscovites were shocked at the loss of convenience stores and questioned why the buildings had been allowed to stand until now.
Mayor Sergei Sobyanin wrote on social networking site VK that the buildings had been "put up illegally" and were "dangerous for Muscovites."
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He said they were "put up mainly in the 1990s with the clear connivance or assistance of officials," a dig at his predecessor in the post, Yury Luzhkov. The sites will now be "beautified," he promised.
The demolitions came as President Vladimir Putin has invoked the need to support small businesses in order to help diversify an economy reeling from falling oil prices.
Nevertheless, "it was always clear that the ownership deeds were temporary and the city hall could destroy these stores if it judged they spoiled the urban landscape," she added.
Opposition politician Alexei Navalny wrote on his blog that it was "impossible to build all this without papers, permits and bribes" and called for the corrupt officials to be punished.
The city authorities had warned owners that the demolition work was imminent but did not say exactly when, leaving them scrambling to secure stock last night.