Navi Pillay, U.N. high commissioner for human rights, said about 30 percent of those killed by militants in eastern DRC were children, which amounted to what she said were "systematic" human rights abuses.
"The Congolese authorities must take immediate measures to protect civilian populations and to combat the persistent impunity which only serves to embolden the killers," she said in a statement.
U.N. investigators said the executions took place from April to September. Much of the violence was allegedly carried out by armed groups allied with the Mai Mai militia.
In October, Human Rights Watch accused the Mai Mai militia of widespread sexual violence in DRC. The group, Human Rights Watch said, killed many of their victims because of their ethnicity.
The United Nations said a rebellion by former soldiers who joined the March 23 movement was a preoccupation for the Congolese military.
The U.N. investigation was reportedly hindered by violence on the ground and an accurate count of civilian deaths was impossible to determine.