The UN human rights group said civilians had been kidnapped, burned and beheaded in IS-controlled areas, with "widespread" attacks on Sunnis suspected of supporting the jihadists.
"We have received reports that some 16 mass graves containing the bodies of individuals murdered by ISIL have been discovered in Sinjar," said Cecile Pouilly, spokeswoman for the UN human rights agency, using an alternative acronym for IS.
It is not clear how many bodies were in the graves and where exactly in Sinjar they were located, she told reporters in Geneva.
The United Nations has described the attack on the Yazidis, whose faith IS considers heretical, as a possible genocide.
Forces from Iraq's autonomous Kurdish region, backed by air support from a US-led coalition, recaptured Sinjar from IS in a major operation on November 13.
Pouilly meanwhile warned that many of the Sunni Arab communities in parts of Iraq reclaimed from IS were suffering increasing human rights abuses.
"Sunni Arab communities have faced increasing discrimination, harassment and violence from other ethnic and religious groups who accuse them of supporting ISIL," she said.
Pouilly described the attacks as "widespread" and told AFP they were particularly prevalent in Anbar, Diyala, Kirkuk, Salah al-Din and in the Kurdistan region.
"This has been going on for months, little by little as territories have been liberated from IS," she said.
She voiced particular concern for some 1,300 Sunni Iraqis stuck to the east of Sinjar in a "no-man's land between Kurdish security forces and ISIL."
