Syrian government backers Iran and Russia, and rebel supporter Turkey, on Thursday signed a deal during talks in Kazakh capital Astana setting up four "de-escalation zones" in Syria.
But neither the government nor the rebels were direct signatories to the deal, and the opposition's reaction was lukewarm.
The HNC, in a statement, expressed "its concern about the ambiguity of the Astana agreement which was reached without the Syrian people and lacks safeguards and compliance mechanisms".
It said the agreement "lacks the minimal elements of legitimacy" and also rejected any role for government ally Iran as a guarantor of the deal.
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"We do not at all agree that Iran... Is a guarantor of this accord," said rebel spokesman Osama Abu Zeid yesterday.
Several members of the rebel delegation left the room shouting in protest as the signing ceremony got underway in Astana, also angered by Iran's role.
The deal calls for the establishment of four "de- escalation" zones across stretches of eight Syrian provinces.
Security zones on the edges of the areas would be set up to monitor and ensure access, with forces from the three guarantor nations manning checkpoints and observation posts.
But it calls for continued action against IS as well as the former Al-Qaeda affiliate now known as Fateh al-Sham Front.
The deal is the latest bid to end more than six years of conflict that have killed over 320,000 people since anti- government protests erupted in March 2011.