Sergei Sobyanin, the city's mayor, said students from the sixth to the 11th grade would be taking online classes for a two-week period starting on Monday, while younger students would continue attending school as usual.
For the past two weeks students have been on a holiday designed to prevent them from contracting the virus and taking it home.
Sobyanin said older students would be studying online at home because they accounted for two-thirds of children infected with the virus.
"The decisions that we have made today are not easy but are simply necessary taking into account both the epidemiological situation and the need for schoolchildren to receive a quality education," he wrote on his website.
Health Minister Mikhail Murashko said the coronavirus situation in the country remained extremely strained and that many people were not following all safety guidelines.
Since the start of the pandemic, Russia has recorded 1,340,409 infections, the fourth largest number of cases in the world behind the United States, India and Brazil.