Citing sanitary violations, the group closed eight of the restaurants by Thursday and 12 by Friday. The company said there are currently 100 outlets under inspection.
"We are studying the essence of claims laid to us to determine the actions necessary to open the restaurants for our customers as soon as possible," McDonald's said in a statement.
Rospotrebnadzor head Anna Popova denied that the closures were politically motivated, but critics of the Kremlin believe it was in response to the sanctions imposed by the U.S. and Europe. Tensions intensified after the U.S. accused Russia of invading Ukraine and threatened further sanctions.
The iconic McDonald's in Pushkinskaya Square, which first opened in 1990 just before the fall of the Soviet Union.
After the U.S. accused Russia of sending troops into Ukraine, Russian President Vladimir Putin said the country "must be forced into substantive talks" with the separatist faction in Ukraine.