Zeid Ra'ad al-Hussein said the government response had so far fallen short.
In March, the decapitated bodies of 40 policemen were found, as well as the bodies of two missing UN investigators.
The government has been fighting the Kamuina Nsapu militia in the region.
Fighting broke out in June last year after its leader Jean-Pierre Pandi called for a popular uprising with the aim of removing all state institutions and security forces from the region so that he could establish his chiefdom.
Mr Pandi was killed two months later, after security forces raided his home, and his followers then took up arms.
The UN says hundreds of people have been killed and more than a million displaced in central DR Congo since fighting broke out.
It says at least 42 mass graves have been found.
It had asked the government to agree to a joint investigation by 8 June, failing which it would call for an international investigation.
DR Congo has been plunged into a constitutional crisis since President Joseph Kabila refused to step down after his term ended last year.
A succession deal brokered by the Catholic Church, that would see Mr Kabila hand over power by the end of this year, has failed to resolve the crisis.
The UN human rights chief has called for an international investigation into massacres and crimes in Democratic Republic of Congo's central province of Kasai.