It did not give a time for the killings and said it was investigating.
Mission chief Martin Kobler said in a statement he had “serious concern over the allegations of the gross human rights violations deemed unacceptable. Any person involved in such acts should face justice”.
He said the crimes had been “committed mainly by armed groups to spread terror”.
Millions of people have died from violence, disease and hunger in eastern Congo since 1996 in conflict fuelled by foreign powers and a struggle for the region’s deposits of gold, diamonds, copper, cobalt and uranium.
Much of the fighting has been in North and South Kivu provinces, which border eastern neighbours including Uganda and Rwanda.