The agencies issued a news release that said the protests have forced them to suspend clean water projects in slum areas and cancel flights to deliver soap and other supplies to affected areas, CNN reported Wednesday.
Demonstrators in Haiti's second-largest city of Cap Haitien set a police station on fire during a second day of protests Tuesday. Thick black smoke from burning tires and cars hung over the city.
Nigel Fisher, the humanitarian coordinator for aid agencies, said supplies were running out in Cap Haitien and the rising cholera mortality rate has overwhelmed the medical staff.
"We call upon all involved in these clearly orchestrated demonstrations to stop immediately so national and international partners can continue to save lives with our response to the cholera," Fisher said.
Haitians charge the cholera outbreak began after U.N. peacekeepers from Nepal allowed untreated sewage to enter the water supply.
The United Nations has denied the charge and said the protests may be politically motivated to create insecurity ahead of Haiti's Nov. 28 elections.