Regime-backer Moscow has invited 1,600 delegates to the meeting in the Black Sea resort of Sochi as part of a broader push to consolidate its influence in the Middle East and start hammering out a political solution to the conflict.
But Syria's main opposition group and Kurdish authorities said they would boycott the event, while today separate rebel representatives were at Sochi airport but refused to come to the congress before Russia met demands.
The Russian and Turkish foreign ministers spoke twice on the phone in a bid to resolve the problem, he said.
A rebel source told AFP that Russia had promised to change or remove the symbol of the congress, which features only the Syrian regime flag.
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But the airport, the road to the conference centre and the congress hall itself were still decorated with banners and billboards bearing the logo when the rebels arrived last night, leading to hours of ongoing negotiations.
Moscow said Syrian society would be fully represented at the meeting -- the first of its kind held in Russia -- but almost all confirmed delegates are from either President Bashar al-Assad's ruling Baath Party, allied movements or the regime's "tolerated opposition".
The Syrian Negotiation Commission (SNC), the country's main opposition group, said following two days of UN-led talks in Vienna last week it would not attend the Sochi congress.
Authorities from Syria's Kurdish autonomous region said at the weekend they would also boycott the event because of the ongoing Turkish offensive on the Kurdish enclave of Afrin.
Clashes and air strikes again hit the border region of Afrin yesterday, with new civilian casualties reported.
Turkey, which supports Syrian rebels vying for Assad's ouster, is co-sponsoring the congress along with regime-backer Iran.
However, members of the opposition were at the event in an individual capacity, while the Kremlin's special envoy on the Syria peace process Alexander Lavrentyev said some Kurds would also attend individually.
The US State Department yesterday said it would not send observers to the Sochi conference, saying "our collective focus must remain on the UN-led political process".
But Mohannad Dleikan, a representative of the Syrian opposition's so-called Moscow Group, which is attending Sochi but which has been accused by the mainstream opposition of toeing a more conciliatory line on Assad's future, said the aims of the talks were the same as those of the UN.
"We have obtained sufficient guarantees that this process will support Geneva, it will not act as an alternative."
Moscow, which has spearheaded several rounds of talks from the start of last year in Kazakhstan's Astana, initially hoped to convene the congress in Sochi last November but those efforts collapsed following a lack of agreement among co- sponsors.
Moscow's decision to launch a bombing campaign to support Assad in September 2015 -- Russia's first major military operation abroad since Soviet troops withdrew from Afghanistan in 1989 -- is widely seen as a turning point in the multi- front conflict that helped shore up the Syrian president.
The Syrian war, in which more than 340,000 people have died and millions more been displaced, began in 2011 as the regime crushed anti-government protests.