However, they disputed even the basic facts, and the opposition delegate told Reuters that international mediator Lakhdar Brahimi met the two parties separately later in the day. These sessions would prepare for the more contentious political talks on Monday on the 2012 "Geneva 1" accord, the delegate, Ahmad Ramadan, told Reuters.
Geneva 1 called for the establishment of a transitional governing body in Syria by mutual consent. The opposition says that means Assad must go, a demand the government has dismissed out of hand, adding to pessimism over whether the Geneva talks can make much progress on ending the civil war.
Following the first face-to-face talks on Saturday and Sunday morning, Ramadan said the government side had yet to respond to opposition demands to release thousands of prisoners taken during almost three years of conflict and to allow humanitarian aid into the city of Homs.
"It has been decided that there will be two preparatory separate sessions in the afternoon for Geneva 1 talks tomorrow," he said. "These sessions will be about political negotiations and about the agenda of implementing Geneva 1 with all its articles so that we can start talks tomorrow."
Another opposition delegate confirmed Ramadan's comments.
Russia, one of the talks' sponsors, had said any agreement on easing the humanitarian crisis would help to improve the atmosphere in Geneva, but acknowledged that positions were polarised, emotions were on edge and the situation remained extremely grave.
Underlining the immense difficulty of implementing even local agreements on the ground, a UN agency trying to deliver aid to a besieged district of Damascus said state checkpoint officials had hampered its work, despite government assurances it would allow the distributions.
In Geneva opposition figures said they presented a list of 47,000 detainees whose release they are seeking, as well as 2,500 women and children whose freedom they say is a priority.
They also wanted the government to allow aid into the rebel-held centre of Homs, besieged by Assad's forces for 18 months, where the opposition says 500 families urgently need food and medicine.
However, Damascus denied having even got the list. Syrian TV cited a government source as saying Damascus was ready to release any civilians "but the coalition of what is known as the opposition has refrained from presenting a list".
Homs was one of the early centres of protest against Assad's rule which erupted in 2011 before Syria slid into civil war. Since the start of the crisis more than 130,000 people have been killed, two million have become refugees and around half the country needs aid, the United Nations says.
Russian Foreign Minister Sergei Lavrov said earlier he hoped the talks could be conducted in a more business-like manner after the two sides exchanged bitter recriminations during a preliminary day of speeches last Wednesday.
In an interview with NTV television, he called for progress on aid, unblocking besieged areas and prisoner exchanges.
"All this would strengthen trust and affect the atmosphere at the talks in Geneva. Beyond this it is very difficult to make guesses; the situation is extremely grave, positions are polarised, emotions are on the edge," he said in comments posted on the Foreign Ministry's web site.
Humanitarian efforts in Syria have been hindered by fighting and by combatants on both sides, who often try to block deliveries to areas held by their opponents.
The UN Relief and Works Agency (UNRWA) complained about problems in delivering deliver food and other aid to Yarmouk, a district of Damascus that is home to impoverished Syrians and Palestinians despite government assurances.
"The agency is extremely disappointed that - at this point - the assurances given by authorities have not been backed by action on the ground to facilitate regular, rapid entry into Yarmouk," spokesman Chris Gunness said. Faced with finding common ground between two intractably opposed parties, Brahimi had dedicated the first two days of talks to humanitarian issues, hoping to create a platform on which to build the far tougher political talks. He plans to start addressing on Monday what he has called the core issue of the talks - implementing the June 2012 accord.