The attack in Oicha, about 30 kilometers (18 miles) from Beni, took place overnight, said Beni territory administrator Donat Kibwana. He blamed the Uganda-based Allied Democratic Forces rebels, who have killed more than 1,500 people in and around Beni in the past four years.
"We have reinforced the military presence in the territory of Beni, but also the army has pursued the rebels," he said. "We call on the population to remain calm."
This week's protests in Beni, after repeated rebel attacks, have turned deadly while disrupting crucial efforts to contain the yearlong Ebola virus outbreak in the region that has killed more than 2,100 people.
Three protesters have been killed by police and four others killed by U.N. peacekeepers trying to disperse the crowds, a civil society spokesman, Ghislain Muhiwa, asserted.
The U.N. mission in Congo "came to kill us or to protect us?" he said. "The choice is simple: Either they fight the enemy or they go home."
More than 5,000 people marched with the LUCHA civil society group Wednesday in Beni, honoring one member who was killed.
The International Committee of the Red Cross called for calm and restraint, saying health care workers should not be targeted. It said that since Nov. 19, facilities supported by ICRC teams have treated five people wounded in attacks in Beni and another 27 wounded in demonstrations.
The violence forced Ebola responders into lockdown in Beni, according to the World Health Organization, which evacuated 49 of its staffers but left 71 in place.
The U.N. mission, accused of inaction, has said it cannot carry out operations unilaterally in a region where Congo's military is already active, and that it cannot participate in Congolese military operations without being invited.
After an emergency meeting Monday, Congo's President Felix Tshisekedi decided to allow joint operations between Congolese and U.N. forces in Beni following the protests that also burned the town hall.
"We have people that manipulate the suffering of the people and use it against the government or against (the U.N. mission)," U.N. envoy Laila Zerrougui told reporters on Tuesday. "We are the scapegoat. We know that."
She said the U.N. was investigating the death of a protester on Tuesday who she said was armed with a petrol bomb and trying to enter the U.N. compound.
Some residents believe the U.N. mission has more resources than Congolese forces and should be doing more, Zerrougui said.
"But the reality is that a peacekeeping mission is not deployed in a country to wage war," she said. "We cannot afford to go and bombard and kill people and then the day after you have photos of children and women massacred in a bombardment by the U.N. ... A government can do that and say this is collateral damage. We cannot do that. We cannot afford to do that. And it is not acceptable that we do that."