The protests apparently began in Cap-Haitien early Monday and within hours had paralyzed much of the northern port city. Other protests broke out in surrounding towns.
The U.N. said the protests are politically motivated, because of the approaching Nov. 28 election. Local reporters said a police station was burned in Cap-Haitien and rocks thrown at peacekeeping bases.
Many in Haiti resent the U.N. military force that has been in the country since 2004.
The U.N.'s World Health Organization said in Geneva on Tuesday that efforts should focus on controlling the disease, not determining where it came from.
Cholera had never before been documented in Haiti before it broke out in October.
More than 14,600 people have been hospitalized as the disease has spread across the country. Officials said on Tuesday that the death toll from the outbreak has passed 1,000.
The Associated Press Contributed to this report.