A statement on the government’s website said an exception would be made for repatriation flights bringing Russian citizens home from abroad, or for flights given special government permission.
The measure came as the number of Covid-19 cases in Russia grew rapidly this week after officials registered 163 new cases on Wednesday, bringing the country’s total confirmed cases to 658.
In previous weeks, cases had been growing by just several dozens a day.
Earlier this month, Russian authorities limited air traffic to regular flights to world capitals and charter flights.
On Wednesday, Vladimir Putin, Russia’s president, said he would postpone a vote on constitutional changes, scheduled for 22 April, which would have allowed him to run for office again amid concerns about the coronavirus pandemic.
“The absolute priority for us is the health, life and safety of people. Therefore I believe that the vote should be postponed until a later date,” Mr Putin said.
The president also announced Russian citizens would not go to work next week in an attempt to slow the spread of the virus.
Although Russia has so far avoided a widespread outbreak of the kind seen in Italy and Spain, he warned it would be impossible to completely prevent the spread of the virus.
Mr Putin ordered snap checks on the readiness of Russian troops to deal with coronavirus earlier this week in a potential sign that his government was preparing for a serious outbreak.
Sergei Sobyanin, the mayor of Moscow, has also said all shops except pharmacies and grocery stores will close in the capital city from 28 March to 5 April because of the pandemic.
His announcement came after he told Mr Putin that the situation in the capital was now serious and authorities were dealing with “significantly more ill people” due to the virus.
Additional reporting by AP
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