The pressure on the American chain, which has 435 restaurants in Russia, comes at a time of heightened tensions over the fighting in eastern Ukraine.
After the United States and the European Union slapped sanctions on Russian state banks and major industries last month, Russia responded with a wide-ranging ban on food products imported from those countries.
Inspections took place or were planned in dozens of regions, Russian news agencies reported, quoting regional representatives of the federal regulatory agency, Rospotrebnadzor. It was unclear how many restaurants were affected, and whether any of them were closed down as a result.
On Wednesday, the agency ordered four Moscow restaurants to suspend operations, citing numerous violations of sanitary laws. McDonald's said only three of those restaurants were closed.
One of those restaurants, on Moscow's central Pushkin Square, was the first to open in the Soviet Union in 1990, drawing crowds of thousands that circled around the block. The restaurant became a symbol of reform and openness with the West, and today it is one of the company's most visited venues in Russia.
News reports on Russian state television, which plays a powerful role in shaping public opinion, included interviews with passers-by who offered their opinions on the unhealthiness of the restaurants' fast food and noted that Russia now has plenty of homegrown alternatives.
In a statement posted on the Russian version of its website Wednesday, the company said it was studying the regulatory agency's complaints to determine what needed to be done to reopen the restaurants as soon as possible. McDonald's 435 restaurants in Russia include 115 in Moscow, where some 12,000 people are employed.