Troops attached to the UN mission, known as MONUSCO, killed one person during a protest in the rural area of Oicha, its mayor Nicolas Kikuku told Reuters.
"They (the protesters) set fire to two bridges that lead to the (peacekeepers') base," Kikuku said. "The MONUSCO peacekeepers did not accept that and opened fire directly on the demonstrators."
Rosette Kavula, the deputy administrator of Beni territory, where Oicha is located, and Philippe Bonane, a local activist, also said peacekeepers had killed a protester.
The incident came after days of protests in several eastern Congo cities by young people angered over the 12,000-strong UN mission’s failure to prevent a wave of civilian killings by armed groups.
MONUSCO spokesman Mathias Gillmann said the mission was investigating what had happened in Oicha.
The other fatality occurred when protesters closed a road to the city of Beni, blocking the path of an ambulance carrying the body of a man killed earlier in a suspected rebel attack, said local army spokesman Antony Mwalushayi.
"That's how a woman was hit and died on the scene, and her baby was seriously wounded," Mwalushayi told Reuters. He said an investigation had been opened into the incident.
At least seven people were killed in the suspected rebel attack, which officials blamed on the Allied Democratic Forces (ADF), a Ugandan Islamist group that has operated on Congolese soil for decades.
More than 300 people have been killed so far this year in violence in eastern Congo, which is in part an unresolved legacy of a civil war that officially ended in 2003.
UN peacekeepers have been deployed to Congo since 1999 at the invitation of the government.