"Really, it's not right, there are killings every day," said Kizito Bin Hangi, a local civil society official.
"Young people in Beni city decided to demonstrate. They threw stones on the avenues, burned tires in some neighbourhoods and called on the population to stop all work," he added.
Police said that officers cleared the main roads after protesters barricaded the streets early Thursday morning.
The killings reportedly stem from armed groups and criminal gangs who use the Beni region of North Kivu province as their battleground, as they fight for mineral resource, including the Allied Democratic Forces (ADF).
ADF has been blamed for killing several hundred people.
A number of attacks occurred on Wednesday, after unknown assailants killed six people in Mbau commune.
"The enemy arrived suddenly last night around 8:30pm... six people were killed while fleeing. Noella Katongerwaki, president of the civil society for Beni territory, told Agence France Presse newswire.
“I saw the bodies of five men and one woman. Four were killed by bullets and two by machete," she said, adding that two women and three children are also missing.
The army confirmed the civilian death toll.
Five people were also kidnapped in Myele village on Wednesday, said Katongerwaki.
Another protest also took place on Wednesday as demonstrators travelled 15 kilometres to deliver a letter to the office for the UN Mission in the DRCongo (MONUSCO) regarding the killings.
In addition to the killings and kidnappings, Beni is ground zero for the Ebola epidemic that has killed more than 1,800 people in the last 12 months.