"Several people died" but the exact toll was "in dispute", with estimates ranging from around 20 to 60 people killed in attacks between April 30 and May 4, the United Nations Office for the Coordination of Humanitarian Affairs (OCHA) told AFP.
An NGO source said the Red Cross had already buried "more than 20" victims.
The aid group could not be reached Friday for confirmation.
The violence in Nyunzu, in the mineral-rich Katanga province, kicked off when vigilantes from the Luba ethnic group, who are Bantu, attacked communities of people displaced by previous bouts of intercommunal violence.
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"The Pygmy situation... Must be taken very seriously," said Rogatien Kitenge, head of an association that defends the rights of Pygmies, warning the hunter-gatherer Pygmies were being "hunted down like game".
The UN peacekeeping mission in DR Congo, MONUSCO, said Wednesday that Pygmy militia had repeatedly attacked Luba villages.
Since colonial times, the Pygmies have cohabited uneasily with the Bantus, who are accused of exploiting the Pygmies, paying them meagre wages -- or with alcohol and cigarettes -- and generally treating them as inferior beings.