Syrian state television said Foreign Minister Walid Muallem had told UN mediator Lakhdar Brahimi that "should serious sessions fail to take place tomorrow, the official Syrian delegation will leave Geneva."
Muallem told Brahimi "the Syrian delegation is serious and ready to start, but the other side is not," it said.
Pulled together by the United Nations, Russia and the United States, delegations from President Bashar al-Assad's regime and the opposition had been due to sit down today at UN headquarters in Geneva.
But UN officials said he had failed and would again meet separately with each delegation.
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"This process is shaping up, so there have been changes to previous declarations," UN spokeswoman Alessandra Vellucci told reporters. "We are going step by step."
The UN said Brahimi had met with the regime delegation and would see the opposition around 4:00 pm (1500 GMT).
Sources within the delegations told AFP the opposition had refused to sit in the same room unless the regime accepted the need for a transitional government without Assad.
"The problem is that these people do not want to make peace, they are coming here with pre-conditions," he told reporters. "Of course we are ready to sit in the same room. Why are we coming here then?"
Nazir al-Hakim, a member of the opposition delegation, told AFP it was only willing to negotiate on the basis of the agreement reached at the "Geneva I" peace conference in 2012, which called for the creation of a transitional government.
"We agree to negotiate on the application of Geneva I. The regime does not accept that," he said.
The regime rejects the opposition's contention that the Geneva I agreement requires Assad to go.
Expectations are very low for a breakthrough at the Geneva II discussions, which officials have said could last up to 10 days. But diplomats believe that simply bringing the two sides together for the first time is a mark of progress and could be an important first step.