"According to interviews with the medical personnel, local authorities and alleged victims, the troops raped 121 women. They also committed acts of looting," deputy spokesman Farhan Haq told a briefing in New York.
"The information was gathered by UN mission members and UNHCR staff," he said, referring to the UN High Commissioner for Refugees. A second mission is expected to go to Niakele in coming days, the spokesman added.
Shortly after the attacks, area lawmaker Jean-Marie Ngoma said Colonel Niragire Kifaru and the roughly 200 fighters under his command were responsible.
Colonel Vianney Kazarama, spokesman for the DRC's armed forces (FARDC) in South Kivu, had previously denied that Colonel Kifaru was involved in the rapes.
Kazarama admitted that Kifaru had deserted and "taken to the bush, because he wanted troops (being integrated into the regular army) to be taken into consideration, because they had no water and nothing to eat."
Kifaru is a former member of the Mai Mai tribal militia who integrated into the national army.
The UN, rights groups and foreign governments have long complained about impunity for heinous crimes committed by soldiers in the DRC.
Margot Wallstrom, UN's special representative on combating sexual violence in conflict, has in the past called DRC the "rape capital" of the world.