"In areas controlled by extremist factions, we are gravely concerned with the mounting number of civilians who perish during air strikes," said Paulo Sergio Pinheiro, who heads the UN Commission of Inquiry on Syria.
"We note in particular that the intensification of air strikes, which have paved the ground for an SDF (Syrian Democratic Forces) advance in Raqa, has resulted not only in staggering loss of civilian life, but has also led to 160,000 civilians fleeing their homes," he told the UN Human Rights Council.
Tens of thousands of civilians have fled Raqa and its surroundings since the US-backed SDF began its operation to capture the jihadist stronghold last year.
And new waves of displacement are expected as the battle inside the city progresses.
"The imperative to fight terrorism must not, however, be undertaken at the expense of civilians who unwillingly find themselves living in areas where ISIL is present," Pinheiro said, using another acronym for IS.
Signup to our newsletter and follow us on Facebook and Twitter!
The UN's Syria commission, which was set up in 2011 shortly after the civil war began, has repeatedly accused the various sides of a wide range of war crimes and in some cases crimes against humanity.
On Wednesday, Pinheiro said a range of deals that have led to evacuations of rebel-held districts and towns in Syria "also raise concerns and in some cases amount to war crimes".
A number of evacuation agreements have been struck for Aleppo and towns and villages around Damascus, as well as in third city Homs.
The government says the deals are the best way to end the six-year war, but the opposition says this amounts to forced displacement.
Pinheiro, who already warned in March that the evacuation from Aleppo amounted to a war crime, said Wednesday that "there is no voluntariness nor choice when those who stay often face the risk of being either arbitrarily arrested or forcibly conscripted".
"In despair, civilians see no option but to leave," he added.
More than 320,000 people have been killed since Syria's conflict erupted in March 2011 with demonstrations against President Bashar al-Assad.