Foreign Minister Walid Muallem said the opposition representatives were immature, while the opposition’s Louay Safi said the regime had no desire to stop the bloodshed.
However, UN envoy Lakhdar Brahimi said he had seen some “common ground”, and scheduled more talks for February 10.
The opposition has agreed to take part, but Walid Muallem refused to commit.
“We represent the concerns and interests of our people. If we find that [another meeting] is their demand, then we will come back,” he told reporters.
He railed at the opposition, saying they had tried to “implode the conference” by insisting that the government hands power over.
Louay Safi said the opposition would not sit in talks “endlessly”, and urged the government to “talk seriously about transferring power”.
Opposition leader Ahmed Jarba said he and his colleagues had “stood up to the regime, a regime that only knows blood and death”.
The two sides discussed humanitarian issues and possible ways to end the violence.
They made some agreements on local ceasefires to allow access for humanitarian workers.
UN aid chief Valerie Amos said the deals had allowed some aid to get through to a few thousand families.
But she said that, so far, an agreed ceasefire in the besieged city of Homs had not had any effect, and no aid has got through.
Parts of Homs have been under government siege for more than 18 months. More than 100,000 people have died in Syria since the uprising against President Bashar al-Assad began in March 2011.
Lakhdar Brahimi said: “Progress is very slow indeed, but the sides have engaged in an acceptable manner. This is a very modest beginning, but it is a beginning on which we can build.”
Though the gap between the two sides was “wide”, they had become used to sitting in the same room, he said.
“There have been moments when one side has even acknowledged the concerns and difficulties of the other side,” he said.
The first round of talks between the government and the opposition National Coalition began last week.
Both sides agreed to use a 2012 document known as the Geneva Communiqué as a basis for discussions, and agreed to meet in the same room.
But neither side could agree on the focus, with the opposition insisting that political transition was the focus, and the government wanting to talk about terrorism.
Diplomats described the atmosphere between the two sides as extremely tense all the way through the conference.
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