The federal agency Rosaviation said the ban on flights over Syria went into force yesterday and will remain until further notice.
"The federal air transport agency believes that in this situation commercial interests cannot prevail over the safety of people who use the services of Russian airlines," it said in a statement.
The ban comes after the crew of a charter plane flying from the Egyptian resort of Sharm-el-Sheikh to the Russian city of Kazan yesterday said it had come under threat when it flew over Syria.
The Interfax news agency, citing a source in Moscow, said unidentified assailants fired two land-to-air missiles at the plane. The aircraft did not suffer any damage and landed in Kazan on time.
The Russian foreign ministry said it had asked the Syrian government to provide a full explanation of the incident.
Rosaviation said a number of airlines had already stopped flying through Syrian airspace after the agency first issued a warning in February. But a number of carriers continue flying over the country, the agency said.