Maurice Mabele Musaidi, a civil society leader in the Democratic Republic of Congo told Reuters that other villagers fled the attacks but may have drowned as they tried to cross the Lamia river into Uganda.
"There are still people missing," Musaidi said.
Musaidi and a spokesperson for Congo's army said the attack in Beni territory's Watalinga chiefdom was carried out by the Allied Democratic Forces, ADF, an armed group based in eastern Congo that has pledged allegiance to Islamic State.
The ADF formed in Uganda before moving over the border in the 1990s and has been blamed for thousands of killings in the last decade.
Congo's army said it killed at least six of the militants that night, without going into detail on the operation.
Army spokesperson Antony Mualushayi put the civilian death toll at 11, though he said that figure was provisional.