Fighters from the Allied Democratic Forces attacked villagers in their fields in Ituri province on Thursday, said John Vuleveryo, coordinator of a local civil society group.
They pillaged houses then set them on fire, he said.
Local people found nine bodies on Friday in the village of Elake Nord and another three in Apesiko, but Vuleveryo warned that the toll could rise. Local officials fear there are more bodies in a nearby forest that is not easily accessible.
Matadi Muyapandi, administrator of the Mambasa territory that includes the villages, and a leading local figure Ibra Mugeni also confirmed the toll.
Mugeni said the three people killed in Apesiko had been found "tied up and had been decapitated".
Soldiers had been deployed in the area to allow the corpses to be buried, said Muyapandi.
The ADF are one of dozens of armed groups active in eastern Congo, many a legacy of regional wars fought after the fall of the vast African nation's longtime dictator Mobutu Sese Seko in the 1990s.
The Islamic State group claims the ADF as its central African affiliate. Originally a Muslim-majority coalition of armed Ugandan groups, it is one of the deadliest militias in the region, accused of slaughtering thousands of civilians.
Congolese President Felix Tshisekedi placed Ituri and neighbouring North Kivu province under a state of siege in 2021 in a renewed bid to drive the ADF out of its strongholds.
Under the measures, security officials were tasked with running the local governments, while the DRC also launched joint military operations with Uganda against the ADF in November 2021.
Rebel attacks have nonetheless continued. Vuleveryo regretted that "large-scale operations" were not led in his area where, he said, "citizens die every day".