A plan to evacuate thousands of jihadist fighters and civilians from three besieged districts of Syria's capital was on hold Saturday, a day after an air strike killed a rebel leader.

Zahran Alloush, 44, was the commander of the Jaish al-Islam (Army of Islam), the predominant opposition faction in the Eastern Ghouta rebel bastion east of Damascus.

A senior member of Jaish al-Islam said planes had targeted a "secret meeting" of commanders, and confirmed that Alloush was among those killed.

His death, in an raid claimed by President Bashar al-Assad's regime, was seen as dealing a heavy blow to the nearly five-year uprising and also complicating a fragile peace process.

It also halted the planned evacuation of some 4,000 people, half of them jihadists, from the southern districts of Damascus.

A government official has said the plan would see the evacuees transferred Saturday out of Qadam, Hajar al-Aswad and the besieged Palestinian camp of Yarmuk and into northern Syria.

Those moved are expected to include members of the Islamic State (IS) group and Al-Qaeda-affiliated Al-Nusra Front.

But a security source close to the negotiations told AFP the plan was now on hold.

"Jaish al-Islam was supposed to provide safe passage through areas east of Damascus for the buses heading to Raqa," IS's Syria bastion, the source said by telephone.

"About 1,200 people were supposed to leave today (Saturday), but the death of Zahran Alloush means we are back to square one," he said.

He said buses standing by to transfer the evacuees had left empty and "the plan was on hold until Jaish al-Islam reorganises itself".

- 'Frozen, not cancelled' -

Another source close to the negotiations said there was a delay in implementing the deal but that it was "still in place".

Syrian Observatory for Human Rights chief Rami Abdel Rahman said the deal was "frozen, but not cancelled, because of logistical issues linked essentially to the difficulty of providing safe passage".

The deal came after two months of intense talks between government and district leaders, according to the Britain-based monitor.

Syria's conflict erupted in 2011 with anti-government protests but has spiralled into a multi-sided civil war across the country.

Alloush was a leading figure in the rebel movement in Damascus province, and had been holding a senior-level meeting in Eastern Ghouta when he was killed.

A Syrian security source told AFP "dozens" of rebels died in two rounds of air strikes by Syria's air force with newly provided Russian missiles.

At least 12 Jaish al-Islam members and seven from the Islamist Ahrar al-Sham group were killed.

Hours afterwards, leading members of Jaish al-Islam elected Abu Hammam al-Buwaydani as a replacement, according to the Observatory.

Buwaydani is a 40-year-old businessman and fighter from Douma in Eastern Ghouta who hails from a family with strong ties to the Muslim Brotherhood, the monitor said.

- 'Severe blow' to peace talks -

Backed by Saudi Arabia, the group recently took part in a landmark opposition meeting in Riyadh aimed at forming a united front for eventual talks with Assad's regime.

It has remained firmly opposed to both Assad and IS.

Analyst Karim Bitar said Alloush's death is "a severe blow to the Riyadh negotiations process".

"Given Alloush's authoritarian temper and strong rule, it will take time for Jaish al-Islam to recover from this blow and for the alternative leadership to emerge," he said.

Aron Lund, editor of the Carnegie Endowment's Syria in Crisis website, said: "In a way, Zahran Alloush has been the rare successful centraliser in the Syrian rebel movement."

But with him gone, that cohesion could "unravel", Lund added.

Elsewhere, a coalition of Kurdish and Arab groups said it seized the key Tishreen Dam from IS on the Euphrates River, as well as seven villages on the river's eastern bank, in the northern province of Aleppo.

Syrian Democratic spokesman Talal Sello told AFP dozens of IS fighters had been killed.

The SDF can now cross into IS-controlled territory along the river's western bank, bringing it less than 30 kilometres (20 miles) from Manbij, an IS stronghold.

The Observatory's Abdel Rahman said the SDF had crossed the dam, and "battles are now on the western bank of the river".