Speaking after briefing the Security Council on the peace process, Staffan de Mistura said a partial truce agreed in February was "barely alive," according to BBC News.
Violence in Syria has intensified in recent days, despite the ceasefire.
At least 20 civilians were reportedly killed on Wednesday in government strikes on a hospital and nearby residential building in eastern Aleppo.
Read alsoU.S. acknowledges another 20 civilian deaths in Syria, IraqThe upsurge in fighting in Syria's largest city comes amid reports that government forces, backed by Russian air power, are gearing up for a major offensive there.
The escalation has threatened to derail the UN-brokered peace talks, which resumed last month.
Read alsoRussian forces in Syria fire at least twice on Israeli military aircraft – mediaThe Western-backed opposition delegation, the High Negotiations Committee (HNC), last week suspended its role to protest against alleged ceasefire violations by the government and a fall in humanitarian aid deliveries to besieged areas.
Speaking on Wednesday after a third round of talks in Geneva, Mr de Mistura said the fragile "cessation of hostilities" "could collapse any time".