The overnight attack blamed on rebels from the Allied Democratic Forces group comes as the deadly Ebola outbreak in the east surpasses 2,000 cases.
Authorities in the Democratic Republic of the Congo say at least 13 civilians are dead after rebels attacked a town affected by the Ebola virus outbreak.
Residents on Tuesday blamed the overnight violence near north-eastern Beni on rebels from the Allied Democratic Forces group.
Beni's interim Mayor Modeste Bakwanamaha said two Congolese soldiers also were killed. Spokesman Zachee Mathima said one attacker was killed and a teenage girl was taken hostage.
Violence resumed in the area, in the southeast of the city, shortly after daybreak, he said.
Calm returned by Tuesday morning.
Attacks by various rebel groups have complicated health workers' efforts to contain Ebola in places like Beni, where nearly 200 people have died from the virus since the outbreak was declared in August.
The violence by ADF rebels and Mai Mai militias has hindered efforts to reach some Ebola-affected areas and vaccinate those most at risk.
Alarm as Ebola outbreak reaches 2,000 cases
The deadly outbreak in eastern Congo has surpassed 2,000 cases and is picking up speed.
The number of confirmed cases reached the milestone three times as quickly as it took to reach 1,000.
The outbreak declared in August has killed more than 1,300 people in a volatile region where rebel attacks and community resistance have hurt containment efforts.
World Health Organization spokesman Tarik Jasarevic told reporters in Geneva on Tuesday that the 2,000 figure is a "sad and frustrating milestone. The insecurity is holding us back."
Each attack keeps health workers from the crucial work of vaccinating people and tracking thousands of contacts of victims.
Aid groups including the International Rescue Committee say a "complete reset" is needed in the response to one of the world's most dangerous diseases.