Local civil society representative Bravo Muhindo confirmed more than 25 dead and said many had been beheaded.
Other people were kidnapped, Muhindo said.
Residents in Beni and surrounding villages have been calling for increased security as the ADF rebels stage attacks in the region.
The ADF originated in neighboring Uganda and has long been a threat in eastern Congo. The Islamic State group has claimed some attacks carried out by ADF rebels, but the exact relationship between the groups is not clear.
A Congolese military campaign was launched against the rebels last year and fighters have since dispersed and fled into various parts of eastern Congo, where dozens of armed groups fight over control of the mineral-rich land.
Rebels have responded to the military offensive with increased attacks, killing more than 800 people last year.