Similar attacks have killed at least 179 civilians, researchers say, since the Congolese army launched an offensive on Oct. 30 against the Allied Democratic Forces (ADF), a Ugandan Islamist group active in eastern Congo.
In his State of the Nation address on Friday, Congo President Felix Tshisekedi said the campaign had "dismantled" nearly all of the ADF's sanctuaries and that the rebels were turning to guerrilla tactics out of desperation.
But the government has blamed the ADF for similar attacks going back years, including dozens of night-time massacres since 2014 that have killed hundreds of civilians. Repeated military operations have failed to fully eradicate the group.
Richard Kivanzanga, the deputy administrator of Beni territory, told Reuters he had counted 22 bodies on Sunday in the villages of Baoba and Ntombi.
"The assailants killed women, men and children," he said. "It wasn't possible to evacuate all the bodies today because we had to wait for an escort from the army."
The surge in violence has lead to deadly protests against the army and U.N. peacekeepers for failing to protect them.
It has also complicated efforts to stamp out an Ebola outbreak in the area. Infections have started to rise in areas health workers have been unable to access because of insecurity.The U.S. Treasury imposed sanctions on Tuesday on six members of the ADF, including its leader Musa Baluku. Islamic State has claimed some ADF attacks this year, but researchers say there is a lack of hard evidence linking the two groups.