Jan Kubis told the Security Council that evidence of the "heinous crimes" committed by the jihadists in Iraq were being uncovered as territory is retaken from IS.
"More than 50 mass graves have been discovered so far in several areas of Iraq," he said.
Iraqi forces, with backing from the US-led coalition that carries out daily air strikes against IS, have retaken significant ground from the jihadists in recent months.
In the city of Ramadi, three graves containing a total of up to 40 sets of remains were found in a football field on April 19, said Kubis.
Ramadi was declared liberated when Iraqi forces seized the main government compound back from the IS late last year, but the city was completely retaken only in February.
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The envoy said the humanitarian crisis was worsening in Iraq, with nearly a third of the population, or over 10 million people, now requiring urgent aid -- double the number from last year.
He projected that a further two million people could be displaced by the end of the year by new military campaigns aimed at driving out the Islamic State group.
Iraqi and Kurdish forces launched an offensive in March in the province of Nineveh, of which IS-controlled Mosul is the capital. The jihadists have held Mosul since June 2014.
Kubis urged Iraqi leaders to resolve differences that have led to street protests in Baghdad, saying that the turmoil will only help IS maintain its foothold.
"They are the ones who stand to benefit from political instability and lack of reforms," said Kubis.
Last week, protesters in Baghdad stormed parliament after MPs again failed to approve nominees for a cabinet of technocrats to replace the government of party-affiliated ministers.