Russian Deputy Foreign Minister Mikhail Bogdanov also said Moscow is preparing to evacuate thousands of its citizens from Syria, where nearly two years of violent conflict have killed more than 40,000 people and turned Assad into a global pariah.
"An opposition victory can't be excluded, unfortunately, but it's necessary to look at the facts: There is a trend for the government to progressively lose control over an increasing part of the territory," Bogdanov said during hearings at a Kremlin advisory body.
Bogdanov's statement marks a clear attempt by the Kremlin to begin positioning itself for Assad's eventual defeat at a time when rebels are making significant gains.
Opposition fighters have seized large swaths of territory in north Syria and appear to be expanding their control outside of Damascus, pushing the fight closer to the seat of Assad's power in the capital. On Wednesday, the U.S., Europe and their allies recognized the newly reorganized opposition leadership, giving it a stamp of credibility and possibly paving the way for greater international aid to those fighting Assad's forces.
At the same time, international condemnation of the regime has grown more intense as Western officials raise concerns that Assad might unleash his chemical weapons stockpiles against rebels in an act of desperation. On Wednesday, the U.S. and NATO said Assad's forces had fired Scud missiles at rebel areas.
Fyodor Lukyanov, the editor of the magazine Russia in Global Affairs, said Bogdanov's statement may reflect new information about the situation on the ground.
"A public statement like that appears to indicate that the balance is shifting," he said.
Abu Bilal al-Homsi, an activist based in a rebel-held neighborhood of Homs in central Syria, said he is encouraged by Bogdanov's comments because Russia is in a position to know about the strength of Assad's forces.
"The Russians know his capabilities and his military force. Russia knows what warplanes and what weapons he has," Abu Bilal said via Skype. "The Free Syrian Army is on the verge of strangling Damascus and this indicates that the regime is reaching an end," he added, referring to the main rebel fighting force.
Despite Russia's acknowledgement that Assad could lose, Bogdanov gave no immediate signal that Russia would change its pro-Syria stance at the U.N. Security Council, where Moscow has shielded Damascus from world sanctions.
Bogdanov also reaffirmed Russia's call for a compromise, saying it would take the opposition a long time to defeat the regime and Syria would suffer heavy casualties.
"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," he added.
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 on Thursday will likely be seen as a betrayal of these longstanding ties. There was no immediate reaction from Damascus 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.
The evacuation plans come at a time of escalating violence in and around the capital.
A bomb blast Thursday near a school in the Damascus suburb of Qatana killed 16 people, at least half of them women and children, the state news agency, SANA, reported. The government says it 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.
Other explosions Wednesday hit near the Palace of Justice, in the suburb of Jermana and in the upscale Mezzeh 86 district, heavily populated by members of Assad's minority Alawite sect. One of the three killed in that that bombing was a state TV journalist named Anmar Mohammed, SANA said.
Assigning responsibility for the blasts, however, remains difficult because rebels tend to blame attacks that kill civilians on the regime without providing evidence while competing groups often claim successful operations.
Assad's forces, too, appear to be escalating the fight. On Wednesday, two U.S. officials said the army had fired scud missiles from Damascus into northern Syria. The officials spoke on condition of anonymity because they weren't authorized to discuss the matter.
One official estimated the army fired more than a half dozen Scuds.
In Brussels, a NATO official confirmed that the alliance's intelligence indicates the firing of Scud-type missiles.