In the first attack, nine civilians were killed and four injured at Oicha Mabasele near the city of Beni, regional administrator Donat Kibwana told AFP. At the same time, in Eringeti, three civilians were killed, also by suspected militia members, he said.
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Dozens of militias operate in the North and South Kivu provinces of the Democratic Republic of Congo, a vast country the size of western continental Europe.
The group that arose in western Uganda in 1995, has been blamed for massacring hundreds of civilians, killing UN peacekeepers and DR Congo troops, and for a number of kidnappings of medical and other staff.
The army confirmed the attacks on Tuesday and said it was hunting the assailants. But locals were critical.
"We alerted the authorities about the presence of the militias near Oicha several weeks ago," said local representative Noella Muliwavyio, adding the population has been "thrown into a panic".
Resident Pascal Soli, a nurse, said he fled with his four children to the local hospital to hide when the shots rang out and later found out his neighbour had been 'slaughtered'.
Several inhabitants of Oicha have fled their homes to the city of Beni, witnesses told AFP.
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