The fate and whereabouts of former Syrian dictator Bashar al-Assad remained unclear on Sunday as his ally Russia, which had long sustained him in office, said he had resigned and departed the country.

“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. It added: “Russia did not participate in these negotiations.”

Assad had not been pictured since a meeting with the Iranian foreign minister in Damascus a week ago when he vowed to “crush” the rebels heading towards the city.

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

There were unconfirmed media reports that Assad had been visiting Moscow late last month when rebels reached Aleppo, 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.

Amid questions over Assad’s whereabouts, Mohammad Ghazi al-Jalali, Syria’s prime minister, told al-Arabia that he had not been able to speak with Assad since Saturday despite claims by state media on that day that Assad remained in Damascus in office.

Hakan Fidan, Turkey’s foreign minister, said on Sunday that he believed Assad was “probably outside of Syria”.

Attention had focused on a flight that left Damascus early on Sunday and disappeared from flight trackers outside Homs, but it was unclear who was on board and whether it had landed.

The head of the Syrian Observatory for Human Rights (SOHR), a UK-based monitoring group, had reported that a plane believed to be carrying Assad “left Syria via Damascus international airport before the army security forces left” the facility.

Rami Abdul Rahman of SOHR said he had information that the plane was meant to take off at 10pm on Saturday. Although there appears to have been no flight at that time, a Syrian Air Ilyushin Il-76T cargo plane did take off from the airport hours later with the Flightradar24 tracking site showing that it first flew east from the capital then north-west before losing altitude near the central city of Homs where the flight transponder signal was lost.

Other reports focused on a flight to Sharjah in the UAE that departed a little earlier but a diplomatic adviser to the Emirati president told reporters in Bahrain that he had no information that Assad was in the country.

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The Russian claim of Assad’s flight from Damascus also prompted multiple conflicting media reports about his destination, with Axios reporter Barak Ravid, citing an Israeli source, claiming the former president flew to a Russian base in Syria on Saturday night, intending to flee to Russia.

The Wall Street Journal reported Assad was already in Moscow with his family following advice from Egypt and Jordan, while Bloomberg suggested a self-exile agreement might involve Assad relocating first to an area under his control and then to Tehran.

Moscow, a staunch backer of Assad, for whom it intervened 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.

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