The Allied Democratic Forces (ADF) carried out the attacks overnight within a seven-kilometre radius (4.3 miles) in the northwest of North Kivu province.
The three villages were attacked simultaneously in an “ADF incursion,” said local leader Macaire Sivikunula.
Villagers panicked as gunfire rang out between 8:00 pm to 10:00 pm, he said, adding that 15 people were killed and 13 houses burned.
Residents who spoke with AFP confirmed the deadly attack.
The Congolese army said two of its soldiers were killed.
“There was an incursion by ADF terrorists in the Bapera sector… the death toll is 14, including 12 civilians and two soldiers,” Lieutenant Marc Elongo, the army spokesperson in the region, told AFP.
The ADF, originally composed of former Ugandan rebels, has been entrenched in northeastern DRC since the mid-1990s, and has killed thousands of civilians.
Ugandan soldiers have been deployed alongside the Congolese army since 2021 to fight the ADF but the joint operation has failed to end the violence.
The ADF primarily attacks defenceless civilians before retreating into the vast forests that cover the region before reinforcements arrive.
