"The fighting will become even more intense, and you will lose tens of thousands and, perhaps, hundreds of thousands of people," he said. "If such a price for the ouster of the president seems acceptable to you, what can we do? We, of course, consider it absolutely unacceptable."
Russia's ties to Syria date back to Assad's father, Hafez, who ruled Syria with an iron fist from 1971 until his death in June 2000. In the last four decades, Russia has sold Syria billions of dollars' worth of weapons. A change in power in Damascus could not only cost Russia lucrative trade deals, but also reduce Russian political influence in Arab world.
The Russians also strongly oppose a world order dominated by the United States and they are keen to avoid a repeat of last year's NATO air campaign that led to the ouster of Libyan leader Moammar Gadhafi, a former Moscow ally.
Bogdanov's remarks will likely be seen in Damascus as a betrayal of these longstanding ties. There was no immediate reaction from the Syrian regime on the comments.
Bogdanov said the Foreign Ministry is preparing evacuation plans for thousands of Russian citizens, most of whom are Russian women married to Syrian men and their children.
"We are dealing with issues related to the preparation for evacuation," Bogdanov said. "We have mobilization plans. We are finding out where our citizens are."
The Interfax news agency said that if the government decides to evacuate Russians from Syria, it could be done by ships escorted by the Russian navy and by government planes.
At the same time, violence was escalating in and around the capital.
The government says the bombing on Thursday in the Damascus suburb of Qatana was the latest in a string of similar bombings in and around Damascus that killed at least 25 people in the last two days.
The government blames the bombings on terrorists, the term it uses to refer to rebel fighters. While no one has claimed responsibility for the bombings, some have targeted government buildings and killed officials, suggesting that rebels who don't have the firepower to engage Assad's elite forces in the capital could be resorting to guerrilla measures.
Similar attacks hit four places in and around Damascus on Wednesday. Three bombs collapsed walls of the Interior Ministry building, killing at least five people. One of the dead was Syrian parliament member Abdullah Qairouz, SANA reported.
Assigning responsibility for the blasts remains difficult because rebels tend to blame attacks that kill civilians on the regime without providing evidence while competing groups often claim successful operations.
Isachenkov reported from Moscow. AP writers Ben Hubbard and Bassem Mroue in Beirut and Slobodan Lekic in Brussels contributed to this report.
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