One motorcycle taxi driver was killed when shots broke out, Beni police spokesperson Nasson Katembo said without giving further details about who was responsible for the gunfire.
MONUSCO said warning shots were fired to disperse protesters throwing rocks at peacekeepers escorted by the Congolese army on their way back from a patrol.
It "deplored" the attack in a statement and said joint investigations with the authorities would shed light on the circumstances that caused the death.
Protesters on motorbikes had gathered and blocked a MONUSCO convoy in Beni - a continuation of violent demonstrations against the mission that have killed dozens, including civilians, peacekeepers and Congolese police elsewhere in eastern Congo since July.
The situation was calm by mid-afternoon, a Reuters reporter said.
U.N. peacekeeping troops have been accused of retaliating with force during the recent protests against them in the eastern cities of Butembo and Goma, which saw hundreds of protesters throw rocks and petrol bombs and set fire to U.N. buildings.
The protests have been spurred by complaints that the peacekeepers have failed to protect civilians against militia violence that has raged for years. The mission has been deployed to Congo for more than two decades and costs more than $1 billion per year.
