Russia has been Assad's main foreign protector during a 22-month uprising against his rule, but a diplomat conceded last month the government had lost territory and the rebels fighting Assad could win the war.
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"On orders from the leadership of the Russian Federation, the Emergencies Ministry is sending two airplanes to Beirut so that all Russians who want can leave Syria," ministry spokeswoman Irina Rossius said.
"It is planned that more that 100 Russians will leave Syria (on these planes)," she told Interfax news agency.
It was unclear whether the flights were the beginning of a longer evacuation operation.
Preparing to fly out its citizens is the clearest signal yet that Moscow believes Assad's fall may be possible, though it has made no indication that it will abandon its position that Assad's exit must not be a precondition for a peace deal.
Moscow leases a naval maintenance and supply facility at the Syrian port of Tartous and has had a large presence of employees from Rosoboronexport, Russia's state arms exporting monopoly.
A number of citizens from Russian companies that also have a presence in Syria still live there too. Russian officials say there are tens of thousands of Russian citizens in Syria, many of them also Russian women married to Syrian men.
Deputy Foreign Minister Mikhail Bogdanov, the Kremlin's envoy for Middle East affairs, said in December the rebels could win the war against Assad and Russia was working on plans to evacuate its citizens, if necessary.
"The regime and government in Syria is losing control of more and more territory," state-run Russian news agency RIA quoted him as saying at the time. "Unfortunately, a victory of the Syrian opposition cannot be ruled out."
Russia's Foreign Ministry said after Bogdanov's remarks that it had not changed its policy on Syria and that he was speaking in a personal capacity.
Russia has protected Assad from three consecutive UN Security Council resolutions aimed at putting pressure on him to end violence from the side of the government. More than 60,000 people have been killed in Syria since March 2011.
The Emergency Ministry told Reuters the planes were scheduled to take off on Tuesday, but that they would leave as soon as they got orders.
Sergei Markov, a political analyst and former lawmaker with President Vladimir Putin's party, said Russia believed Assad will fall and "may believe it is time to start gradually pulling its citizens out".
"Russia is preparing for the collapse of the central government," said Markov, vice-rector of the Plekhanov Russian University of Economics.
At least eight warships from Russia's Northern, Baltic and Black Sea fleets were taking part in the maneuvers.
Russia delivered Assad delivered nearly $1 billion in arms to Syria in 2011. CAST, a Moscow-based defense think tank, said Russia had been due to send half a billion dollars' worth last year.
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