Insurgents believed to be from the Allied Democratic Forces (ADF), a Ugandan armed group that has operated in the dense forests of eastern Congo for decades, attacked a church clinic at around 10.00 pm on Thursday night, the witnesses said.
An army spokesman confirmed the attack in the town of Lume in North Kivu province, but did not say how many people died.
A witness said there were seven dead, while a nurse at the hospital said the provisional toll was 13 and many were still missing.
Uganda has sent at least 1,700 troops to neighbouring Congo to help fight the ADF after accusing the group of responsibility for a string of bombings in Kampala last year.
The ADF killed more than 1,300 people in the last year, mostly in night-time attacks on remote villages, UN experts said.