A Defence Ministry spokesman told Russian news agencies the launch was detected at 10:16 am Moscow time (0616 GMT) by an early warning radar station at Armavir, near the Black Sea, which is designed to detect missiles from Europe and Iran.
"The trajectory of these objects goes from the central part of the Mediterranean Sea toward the eastern part of the Mediterranean coast," Interfax news agency quoted the spokesman as saying.
The spokesman did not say who had carried out the launch and whether any impact had been detected, but RIA later quoted a source in Syria's "state structures" as saying the objects had fallen harmlessly into the sea.
The Russian Defence Ministry declined comment to Reuters.
The Russian Embassy in Syria said there were no signs of a missile attack or explosions in Damascus, state-run Itar-Tass reported.
Israel said it was unaware of any ballistic missile launch being conducted in the eastern Mediterranean.
"We are not aware, at this time, of such an event having occurred," a military spokeswoman in Jerusalem said.
Russian Defence Minister Sergei Shoigu had informed President Vladimir Putin of the launch.
Russia opposes any outside military intervention in the Syrian civil war, and a Defence Ministry official had earlier criticised the United States for deploying warships in the Mediterranean close to Syria.
The United States has been preparing for a possible military strike in Syria following what it says was a chemical weapons attack by Syrian government forces. Damascus denies carrying out such an attack.