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The face-to-face meeting had been planned for Friday, but the opposition said early on it would not meet the government side unless it first agreed to sign up to a 2012 statement by world powers calling for a transitional government in Syria.
The government rejected the demand and said its negotiators would leave unless serious talks began within a day.
Even if the talks appear be back on track, few expect the conference to come up with an overall political settlement to the war, given the absence from Geneva of powerful Islamist opposition groups and President Bashar al-Assad's ally, Iran.
After separate meetings with government and opposition delegations, U.N. mediator Lakhdar Brahimi indicated on Friday afternoon their argument, which centres on whether or not Assad would have to step down, had been put on one side.
"Tomorrow we have agreed that we shall meet in the same room," Brahimi told a news conference. The negotiations would be based the 2012 statement, known as Geneva 1, which he acknowledged was subject to differing interpretations.
Brahimi made clear the talks, scheduled to last another week, would not be easy. "We do expect some bumps on the road," he said. "We wanted these delegations nominated months ago to prepare things better."
Diplomats are playing down any hopes of progress.
"Expectations are so low we'll see how things develop day by day," a Western diplomat said. "Every day that they talk is a little step forward."
Brahimi has indicated that his aim is to start by seeking practical steps, like local ceasefires, prisoner releases and access for international aid deliveries, before embarking on the tougher political negotiations.
"I think an immediate political solution is unrealistic, unfortunately," French Foreign Minister Laurent Fabius told France 24 television.
Syria's civil war has already killed at least 130,000 people, driven more than a third of the country's 22 million people from their homes and made half dependent on aid, including hundreds of thousands cut off by fighting.
Among the hurdles to progress, the Islamist militants who control most rebel-held territory are boycotting the talks and say anyone attending negotiations that fail to bring down Assad would be traitors.
Assad's main regional backer, Iran, is also not represented at the Geneva talks. U.N. Secretary-General Ban Ki-moon invited Tehran at the last minute, but then withdrew the invitation 24 hours later when it refused to endorse the Geneva 1 protocol.
On Friday, Iran, accused by Western leaders of backing Lebanese Hezbollah militia who have helped Assad reverse rebel advances, called for an end to foreign interference in Syria, where arms and funds have flowed in from a range of countries.
Fighters from Iraq and elsewhere are also present in a conflict that has become a proxy war for regional powers.
"I can ask all foreign forces to withdraw from Syria, to allow the Syrian people to decide their own future. To stop funnelling money and arms into Syria," Foreign Minister Mohammad Javad Zarif told the World Economic Forum in Davos.
Turkey's Foreign Minister Ahmet Davutoglu also called for the withdrawal of all forces from Syria, including Hezbollah fighters who are backing Assad. "Turkey wants all non-Syrians to leave Syria today, be it Hezbollah or others," he said.
U.S. State Department spokeswoman Jen Psaki welcomed Brahimi's announcement that talks would start on Saturday as a "positive step forward in what we expect will be a long and complicated process".