Russia's foreign minister was heckled at the talks whilst an opposition delegation refused to leave the airport in Sochi.
Russia, a staunch ally of Syrian President Bashar al-Assad, hosted what it called a Syrian Congress of National Dialogue in the Black Sea resort of Sochi on Tuesday in the hope it would launch negotiations on drafting a new constitution for Syria.
But in a blow to Moscow, which has cast itself as a Middle East peace broker, the event was boycotted by the leadership of the Syrian opposition, while powers such as the United States, Britain and France stayed away because of what they said was the Syrian government's refusal to properly engage.
Western countries support a separate U.N.-mediated peace process, which has so far failed to yield progress towards ending a war that is entering its eighth year. The latest round of those talks took place in Vienna last week.
Russian Foreign Minister Sergei Lavrov helped open the conference on Tuesday by reading out a statement from President
Vladimir Putin saying the conditions were ripe for Syria to turn "a tragic page" in its history.
But some delegates stood up and began heckling him, accusing Moscow of killing civilians in Syria with its air strikes.
The incident was broadcast on Russian state TV where two security guards were shown approaching one man in the audience indicating that he should sit down.
Other delegates shouted out their support for Russia. Lavrov told the delegates to let him finish speaking, saying they would have their say later.
In a further setback, one group of delegates, which included members of the armed opposition who had flown in from Turkey, refused to leave Sochi airport until Syrian government flags and emblems which they said were offensive were removed.
Ahmed Tomah, the head of the delegation, said his group was boycotting the congress and would fly back to Turkey because of the flag row and what he called broken promises to end the bombardment of civilians.
"We were surprised that none of the promises that were given had been kept, the ferocious bombing of civilians had not stopped nor the flags and banners of the regime (been) removed," he said in a video recorded at the airport.
Artyom Kozhin, a senior diplomat at the Russian Foreign Ministry, acknowledged there had been some complications.
"Some problems have arisen with a group of the armed opposition that has come from Turkey which has made its participation dependent on additional demands," Kozhin wrote on social media.