The demonstrators were protesting against local forces and UN peacekeepers for failing to stop the Allied Democratic Forces (ADF) militia from killing seven civilians in the town on Wednesday.
Security forces moved in with gunfire and tear gas to disperse the protestors in the northern Boikene district at around 1:30 pm (1140 GMT), an AFP correspondent said.
There was no immediate report of casualties.
Several dozen youths fought back with stones and pieces of wood, trying to get to a base of the UN mission deployed in Congo, MONUSCO. They also accuse UN troops of doing nothing about ADF killers.
Protesters destroyed a wall and ripped off barbed wire that protects the entrance to a camp.
“They have to leave, it’s too much,” said Fiston Katsuva, 20, a protester.
The Beni protests also forced health workers to “put on hold” local efforts to combat an Ebola virus epidemic that has killed more than 2,000 people since it began in August 2018.
“It concerns all our activities: awareness, vaccination, safe burials, etc. But we have not stopped working. We will continue to be present,” said doctor Jean-Jacques Muyembe, who leads the campaign against Ebola.
Ebola-hit provinces of North Kivu, which includes Beni, Ituri and South Kivu, already suffer from chronic insecurity, with various militias operating in the region. Violence has complicated the Ebola response since the outbreak began.
The army three weeks ago announced a “large-scale operation” against strongholds of the ADF rebels, who originated in northern Uganda and form one of a number of armed groups active on the Congolese side of the border.
“I can understand people’s frustration over the last few weeks or even years, but I do not understand how they can attack our facilities, our vehicles, our staff,” said Omar Aboud, the head of the UN office in the region.
Roadblocks, markets closed
The tense standoff in northern Beni was accompanied by a stoppage of normal activities in other parts of the town.
The mayor of Butembo, a trading crossroads town 54 kilometres (34 miles) to the east of Beni, told AFP that demonstrators had blocked roads in solidarity with people in Beni. Buses and taxis were not running and markets were closed.
“Ten people have been arrested,” said mayor Sylvain Kanyamanda. “Police will interrogate them separately to have them explain what they were doing on the public highway this morning.
“We can’t mourn compatriots killed while breaching the peace. In a few moments, order will be restored,” he added.
More than 60 civilians have been massacred in the Beni region since military action against the ADF began at the start of November.
The ADF began as an Islamist rebellion hostile to Ugandan President Yoweri Museveni. They fell back into eastern DRC in 1995 and have recruited people of different nationalities, but appear to have halted raids inside Uganda.