The violence came as officials said more than 1,034 people had now died in the outbreak.
Meanwhile the riots had left at least two people dead and some roads remained barricaded last night.
One demonstrator was shot dead by a UN peacekeeper during an exchange of gunfire in Quartier Morin, near Haiti's second-largest city of Cap-Haitien, the UN mission said.
Haiti senate president Kelly Bastien said a second demonstrator was shot and killed in Cap-Haitien itself.
The 12,000-member force reported at least six UN personnel wounded in protests at Hinche in the central plateau, while local radio reported at least 12 Haitians injured in Cap-Haitien. The protests apparently began in Cap-Haitien and paralysed much of the northern port city.
As the day went on, other protests broke out in surrounding towns and the central plateau. Local reporters said a police station was burned in Cap-Haitien and rocks were thrown at peacekeeping bases. A small protest was also reported in the northwest city of Gonaives, but UN police said it ended peacefully.
The UN stabilisation mission in Haiti, or Minustah, dismissed the protests as political, linking them to the fast-approaching 28 November presidential elections. "The way events unfolded suggests these incidents were politically motivated, aimed at creating a climate of insecurity on the eve of elections. Minustah calls the people to remain vigilant and not be manipulated by enemies of stability and democracy in the country," the mission said in a statement.
Officials said investigations to determine if the protesters' suspicions are correct will have to wait. The World Health Organisation said in Geneva yesterday that efforts should focus on controlling the disease, not determining where it came from.
WHO spokesman Fadela Chaib said that "at some time we will do further investigation but it's not a priority right now".
The UN's spokeswoman in Geneva, Corinne Momal-Vanian, described the suspicion that Nepalese troops were to blame for cholera as "misinformation".
The cholera backlash plays upon long-standing resentment of the 12,000-member UN military mission, which has been the dominant force in Haiti since 2004. It is also rooted both in fear of a disease previously unknown to Haiti and real fears the UN base could have been a source of the infection. Cholera had never been documented in Haiti before it broke out about three weeks ago. Suspicions quickly focused on a Nepalese base on the Artibonite river. They arrived following an outbreak in Nepal, a week before Haiti's first case was reported.The US Centre for Disease Control and Prevention has said that the strain matched one only found in South Asia.