Russia said on Sunday that Syrian President Bashar al-Assad had left office and departed his country after giving orders for a peaceful transfer of power, but did not say where he was now or whether the Russian military planned to stay in Syria.

Islamist rebels declared they had ousted Assad after seizing control of Damascus on Sunday, ending his family's decades of autocratic rule after more than 13 years of civil war.

Assad flew out of Damascus for an unknown destination earlier on Sunday, two senior army officers told Reuters. His current whereabouts were unknown.

"As a result of negotiations between B. Assad and a number of participants in the armed conflict on the territory of the Syrian Arab Republic, he decided to resign from the presidency and left the country, giving instructions for a peaceful transfer of power," Russia's Foreign Ministry said in a statement.

"Russia did not participate in these negotiations."

There were unconfirmed media reports that Assad had been visiting Moscow, where his elder son studied, when rebels reached Aleppo late last month, before returning to Syria. The Kremlin declined to comment on the matter at the time and it is unclear whether Russia has offered him refuge now.

Moscow, a staunch backer of Assad whom it intervened to help in 2015 in its biggest Middle East foray since the Soviet collapse, is scrambling to salvage its position with its geopolitical clout in the wider region and two strategically-important military bases in Syria on the line.

MILITARY BASES

The Kremlin, which convened a conference call with reporters on Sunday to set out its response to a call by U.S. President-elect Donald Trump for immediate talks on Ukraine, made no comment on the unfolding situation in Syria, saying its stance had been set out in the foreign ministry statement.

The ministry's statement said Russia's two military facilities in Syria had been put on a state of high alert, but played down an immediate risk to them.

"There is currently no serious threat to their security," the ministry said.

Russia operates the Hmeimim air base in Syria's Latakia province which it has used to launch airstrikes against rebels in the past, and has a naval facility at Tartous on the coast.

The Tartous facility is Russia's only Mediterranean repair and replenishment hub, and Moscow has used Syria as a staging post to fly its military contractors in and out of Africa.

Losing Tartous in particular would be a serious blow to Russia's ability to project power in the Middle East, the Mediterranean and Africa, say Western military analysts.

Russian war bloggers, some of whom are close to the Russian Defence Ministry and get more freedom from Russian authorities to speak out than military officials, have warned that the bases are now dangerously exposed regardless of what Moscow says officially.

The Foreign Ministry said Moscow was alarmed by events in Syria.

"We urge all parties involved to refrain from the use of violence and to resolve all issues of governance through political means," its statement said.

"In that regard, the Russian Federation is in contact with all groups of the Syrian opposition."

It said it was also doing all it could to ensure the safety of Russian citizens in Syria, whom the embassy on Friday advised to leave the country. The Russian Embassy in Damascus told the state TASS news agency on Sunday that its staff were "fine."