Following the opening speeches, rebel groups refused to sit face-to-face with government representatives, citing the Syrian government's continued bombardments near Damascus.
Instead, both sides spoke through intermediaries.
The delegations were moved into two separate rooms. One is for the opposition and the Turkish representatives, and the other is for the government and the Russians.
Issues about how to stabilise and uphold the ceasefire through dispatching monitors and surveillance equipment were discussed.
"Some of the participants and namely speaking, the delegation of the terrorist armed groups, gave its own interpretation, or misinterpretation of these agreements, and went beyond the framework of these agreements, and that created a problem for all the participants. Because the delegation of the armed terrorist groups did not respect the provisions of the agreement, on the basis which we came to Astana," said Bashar al-Jaafari, head of the Syrian government delegation.
The three-week-long ceasefire across Syria has been fragile; brokered by Russia, Turkey and Iran, who have paved the way for these talks.
The opposition is demanding the release of detainees from government prisons.
These talks come a month after Syrian forces regained control of Aleppo, Syria's second-largest city, which had long been a bargaining chip for the rebels.
There is little expectation of a breakthrough heading into day two, yet these negotiations could set the tone for another round of U.N.-mediated talks in Geneva, Switzerland at the beginning of February.