The Syrian regime and key powerbrokers on Tuesday tried to shrug off the absence of rebel groups as they gathered for talks on the six-year conflict, but the opposition's refusal to attend appeared a body blow for any hopes of progress.

The third round of negotiations sponsored by regime allies Russia and Iran and rebel-backer Turkey come as other diplomatic efforts to end the bloodshed have proved fruitless.

Regime negotiator Bashar al-Jaafari slammed the rebels' decision to snub the talks in the Kazakh capital Astana after attending two earlier rounds but insisted that there was still a point in going ahead with the event.

"We are eager to ensure the success of the Astana path... whether or not the armed factions attend," Jaafari was quoted as saying by Syria's SANA news agency.

"The failure of the armed factions to attend Astana shows the indecency of their politics."

Jaafari said the regime delegation had come to the two-day talks primarily to meet with Russia and Iran, and not armed opposition groups.

Russian Foreign Minister Sergei Lavrov said Moscow thought the rebels' refusal to show up stemmed from a "misunderstanding", local news agencies reported.

But the rebels said earlier that they were skipping the Astana talks in protest at regime violations of a shaky ceasefire in place since the end of last year.

More than 320,000 people have been killed and millions forced to flee their homes since the conflict erupted in March 2011 with protests against President Bashar al-Assad's rule.

UN rights chief Zeid Ra'ad Al Hussein said Tuesday that the Syrian conflict was the "worst man-made disaster the world has seen since World War II".

Two previous rounds of talks in Astana were focused on bolstering a frail nationwide truce brokered by Moscow and Ankara in December that has been jeopardised by fighting across swathes of Syria.

Kremlin spokesman Dmitry Peskov told reporters Tuesday that the talks were "from time to time truly complicated by the existing differences in the different sides' approaches".

A new round of negotiations in Geneva is set to begin on March 23 and will focus on governance, the constitution, elections, counter-terrorism and possibly reconstruction, according to the UN's Syria envoy Staffan de Mistura.

Russian mediator Alexander Lavrentiev said the Astana talks were meant to "facilitate" de Mistura's task of finding a solution to the conflict.

"If this brings any good, we think this will benefit the Geneva process," Russian news agencies quoted Lavrentiev as saying.

As officials met in Kazakhstan, a UN probe accused the Syrian government of intentionally bombing the Ain al-Fijeh spring outside Damascus in December, leaving more than five million in the capital without access to water.

The UN branded the strike a "war crime" and dismissed regime allegations that the rebels had contaminated the water.