Ja'afari called de Mistura's words an "error" that could "derail his mandate as a facilitator of the talks, which will have an impact on the Geneva process altogether".
Ja'afari said the Syrian delegation at the Geneva talks had engaged seriously in the round, which he said had focused on counter-terrorism.
On the outskirts of the Syrian capital, one in eight children are reportedly starving because President Bashar Al Assad's forces, supported by Russian Federation and Iran, continues to block trucks carrying relief supplies.
He noted Thursday that no date has been set for a next round of the Geneva talks, and that said that under current circumstances "I don't think that another round would be quite effective".
On Thursday, the United Nations envoy for Syria says the peace talks in Geneva were a "golden opportunity missed" as another round ended without progress after two weeks.
The U.N. envoy has conducted shuttle diplomacy between the Syrian government delegation led by chief negotiator Bashar al-Ja'afari and a unified opposition delegation.
The Damascus government uses the term to refer to all armed opposition against President Bashar Assad.
Seven previous rounds of talks mediated by De Mistura have also gone nowhere - and the rival sides have not yet met face-to-face.
He blamed the Syrian government delegation mainly, for setting preconidtions on holding direct talks with the opposition, claiming that it would be challenging for any future talks to make progress, "if the government is not willing to meet anyone who has a different opinion".
He said a statement issued by a revamped opposition delegation team in Riyadh ahead of the talks demanded a political transition in which Assad did not participate.
However, on Friday the lack of progress in Geneva and continuing assault of the besieged rebel enclave of Eastern Ghouta near Damascus brought scathing criticism from Paris. He also told reporters in Geneva that "those who drew up the Riyadh communique are the ones who sabotaged this round" of talks.
Russian President Vladimir Putin during a surprise visit on Monday to Russia's Hmeymim air base in Syria, declared that the work of Russian forces was largely done in backing the Assad government against militants, following the defeat of "the most battle-hardened group of worldwide terrorists".
Asked on Swiss broadcaster RTS what signal Putin could provide now, de Mistura alluded to how territorial gains would be "temporary".
Russian Federation has provided crucial military and diplomatic backing to Syrian President Bashar Assad's forces. "The clear impression is the regime wants to avoid the United Nations -led political process at any cost".