Meanwhile, in the ravaged city of Aleppo, government forces and their allies captured new ground on the city's edge, tightening the siege on rebel-held parts of the city.
More than 250,000 people have died and 11 million from a population of 23 million have been forced from their homes in Syria's five-year war which started as an uprising against Assad's rule.
US Secretary of State John Kerry called on all sides to respect the deal, which was finally reached after several failed attempts over recent weeks.
Western countries, Turkey and most Arab states oppose both Assad's government and Islamic State, while supporting other anti-Assad factions.
Footage of the apparent chlorine gas attack on the Sukari district, near Aleppo's main battlefield in the city's southwest, showed crying children being doused with water and then lying on hospital beds and breathing through respirators.
More than 70 humanitarian organizations are accusing the United Nations of allowing the Syrian government to manipulate relief efforts and deprive thousands in besieged areas of help.
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"The Syrian government has interfered with the delivery of humanitarian assistance in multiple instances, including the blocking of aid to besieged areas", the aid groups said.
However, the government has a history of being accused of similar attacks.
The ministry denied any gas attack by the Syrian army on the rebel-held neighborhood of Sukkary, which allegedly took place on Wednesday.
Fighting continues to rage on in southern Aleppo hours after the United States and Russian Federation hailed a breakthrough deal to put Syria's peace process back on track, army officials and rebels say. The activist-operated Aleppo Media Center and the Local Coordination Committees also reported that nine were killed in the bombing.
Speaking shortly after De Mistura, the UN's humanitarian chief, Stephen O'Brien said it was imperative that a way forward was found to meet the humanitarian needs of Syrians in what he described as "a man-made humanitarian crisis".
Insurgents said they were planning a counter-offensive.
