Medicines Sans Frontiers or MSF said IDPs living conditions were extremely poor in UMMISS compound in Juba Na Bari camp known as Tomping.
In a statement issued on Tuesday, MSF said the camp was overcrowded with only ten square meters for every person with major problems of water and sanitation.
It said the conditions intensified the health problems among IDPs as more than 50 people share one latrine, a situation above the emergency standard.
MSF warned that unless residents were moved to a less crowded place with a better drainage system, it will increase water borne diseases and malaria as rain started.
A flooded overcrowded camp would make the situation unsustainable for IDPs who fear attacks at their residents, it added.
MSF said it has the ambition to move part of the residents to Juba Three camp to reduce the conditions.