Warning: some of the material in this report is disturbing.
The UN Human Rights Council in Geneva heard Zeid Ra'ad al-Hussein cite harrowing reports from experts he had sent there to interview refugees from the volatile central Kasai provinces.
The High Commissioner for Refugees described the Kasai region as a "landscape of horror" with various actors, including some state agents, fuelling ethnic hatred.
"Refugees from multiple villages in the Kamonia territory indicated that the Bana Mura have in the past two months, shot dead, hacked or burnt to death and mutilated hundreds of villagers as well as destroying entire villages. My team saw children as young as two whose limbs had been chopped off. Many babies had machete wounds and severe burns. One two-month-old baby seen by my team had been hit by two bullets four hours after birth. The mother was also wounded. At least two pregnant women were sliced open and their foetuses mutilated."
Before the report by the Catholic church, the death toll was thought to be around 400.
But Mr al-Hussein says 42 mass graves have been documented, and there may be many more.
"It is the duty of the Congolese authorities, army and police, to protect the people, to act in accordance with human rights principles and to bring the perpetrators of human rights violations and abuses to justice. Accountability for these shocking incidents must be assured. I regret that to date the Congolese government has not fulfilled these obligations of protection and accountability."
The region in central Congo exploded into violence last September after followers of Kamwina Nsapu - who was killed a month earlier - rebelled against what they saw as increasing repression by the Congolese government.
The tribal chief had previously openly challenged the authority of President Joseph Kabila's government.
An estimated 1.3 million people were forced to flee their homes, with reports of child soldiers also being recruited - some as young as seven.
Earlier this year, two experts sent to investigate the conflict by the UN Secretary-General went missing.
Their bodies were found in a shallow grave by peacekeepers two week later.
The government blamed tribal militias for their murders.
DRC's Human Rights Minister, Marie-Ange Mushobekwa, told the UN Council the government will soon publish its own report on the crisis.
"Some countries should not use the blood of our compatriots for political purposes, or seek to instrumentalise the Human Rights Council, an institution so respectable, to settle accounts to states whose leaders do not like them. May this mass graves case not become a slogan used by some countries today."
But the UN High Commissioner says he wants an inquiry.
"I urge this Council to deploy an independent international investigation on the human rights situation in the Kasais, in cooperation with the authorities, my office and other parts of the UN system. I will also remain in touch with the International Criminal Court."
