Medecins Sans Frontieres (Doctors Without Borders) launched a stinging attack on UN officials in the country, accusing them of leaving terrified civilians in a section of camp acknowledged as a "death trap" because of its potential exposure to diseases.
"We are doing our best to decongest the site and encourage people to move voluntarily to better sites with better sanitation," UN spokesman Stephane Dujarric said.
"It is a huge logistical challenge to take care of these thousands of people."
Nick Birnback, spokesman for the UN Department of Peacekeeping Operations, rejected the MSF criticisms of UN officials in South Sudan.
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"I strongly disagree with the assertions made by MSF against UNMISS and these views are not necessarily shared by the rest of the humanitarian community," Birnback.
"There has been no change in the level of humanitarian assistance being provided," he said.
The UN was keenly aware of the risks of epidemics and overcrowding, he added.
Around 1,500 civilians had moved voluntarily from the area of the Tomping base in Juba posing the greatest of health risks.
MSF earlier argued that the UN was failing to do enough in South Sudan, which has been in conflict since mid-December when troops loyal to President Salva Kiir clashed with supporters of his former deputy Riek Machar.
The war has since spread across the world's newest nation, with thousands seeking UN protection from ethnic massacres by security forces from Kiir's Dinka tribe or rebels from Machar's Nuer people.