Jan Kubis told the UN Security Council that it was “evidence of the heinous crimes” IS had committed.
This comes as the territories had recently liberated from the Islamic State (IS) terrorist group.
“More than 50 mass graves have been discovered so far in several areas of Iraq,” he said.
Kubis noted that three graves containing some 40 sets of remains were found in a football pitch in the central city of Ramadi, the capital of Anbar province, on April 19.
Mr Kubis said the international community should “take steps to ensure the accountability” of IS fighters.
The envoy said the humanitarian crisis is 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.
The northern and western parts of Iraq have been plagued by violence ever since Daesh began an offensive in the Arab country in June 2014.