The arrests were prompted by President Vladimir Putin's announcement that the government would crack down on radical Islamists in anticipation of next year's Winter Olympics in Sochi.
"We must fight back hard against extremists who, under the banners of radicalism, nationalism and separatism, are trying to split our society," Putin said Friday.
Russia's Federal Security Service did not say why that specific prayer room was raided.
Radio Free Europe reported (via Fox News) that police had also confiscated Islamist literature as part of the raid.
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