The Kazakhstan talks are brokered by Russian Federation and Turkey, which back opposing sides in the almost six-year war and have taken the lead with peace efforts since December.
Kazakhstan's Foreign Ministry did not offer an explanation for the change.
The meeting must have been held in a closed format.
The Astana talks are to be followed by a new round of UN-sponsored peace talks in Geneva on February 20.
The U.N.'s envoy on Syria, Staffan de Mistura, said he would not participate personally in the latest Astana meeting but that his office would be represented by a "technical team".
Salim Al-Muslit, spokesman for the High Negotiations Committee (HNC), said there could be no role for Al-Assad in the transition, saying "the heavy price paid by the Syrian people" would have been wasted if he remained.
The Astana initiative has left the West on the sidelines of the latest push to end the war in Syria, which has claimed more than 310,000 lives since 2011 and forced millions of people to flee their homes.
The first round of Astana talks on Syrian settlement was held in the Kazakh capital on 23-24 February 2017 with participation of delegations of Iran, Russia, and Turkey as observers and representatives of Syrian government and a number of armed opposition group.
The talks are likely to focus on bolstering a shaky ceasefire on the ground. Syrian President Bashar al-Assad has previously said he has "high hopes" for increased engagement between the United States and Russian Federation to fight ISIS. At a previous meeting in Astana in January, Russia, Iran and Turkey agreed to serve as the monitors for the cease-fire.