The Moscow office of Russia's powerful consumer safety agency Rospotrebnadzor said inspections of the food and premises at the four restaurants of the US fast food giant found "numerous violations of sanitary legislation requirements".
The announcement comes in the wake of Russian bans on US and EU food imports in response to Western sanctions over Moscow's perceived backing for rebels in eastern Ukraine.
Among the restaurants closed was the first McDonald's opened in the Soviet Union in 1990 off Moscow's central Pushkin Square.
Some 30,000 Soviets queued for hours for a taste of American fast food on the day that restaurant opened, setting a company record.
The company -- which has strived to support the local economy and relies almost exclusively on Russian-produced food -- said in a statement that it was studying the complaints and that "McDonald's top priority is to provide safe and quality products".
McDonald's added that it would do everything possible to ensure the company's continued successful operation in Russia, where it has some 430 restaurants and employs more than 37,000 people.
It only confirmed three restaurants had been closed, however, while Rospotrebnadzor said four were on its list.
One of the restaurants closed was in an underground shopping mall in the shadow of the Kremlin's walls.
- Made in Russia burgers -
Rospotrebnadzor had already last month expressed doubts about the "quality and safety of food products in the entire McDonald's chain" and said it was taking the company to court for quality violations and improper labelling.
That action coincided with Moscow's decision to start banning numerous food products, ostensibly for health reasons, from countries that imposed sanctions on Russia over its backing of rebels in eastern Ukraine.
Russia later banned most food imports from the European Union and United States in a tit-for-tat response to tighter Western sanctions.
Rospotrebnadzor said last month it found violations in two McDonald's locations in the town of Novgorod north of Moscow, including for improper labelling of the food items' calorie contents.
"The products did not conform to standards of safety or food value," Rospotrebnadzor spokeswoman Anna Popova was quoted as saying at the time.
McDonald's said last month it calculates food and energy values of its products based on methodology approved by the Russian Academy of Medical Sciences.
While offering a taste of America, the burger chain has been one of the most aggressive in developing a network of local suppliers, and was in a good position to survive the food sanctions without radical changes to its menu.
The company said earlier this month that over 85 percent of its products were provided by more than 160 Russian suppliers.
"We are continuously studying the possibility of expanding our cooperation with Russian producers," it said in a statement.