Heavy rains and fighting have caused an increase in the number of victims falling prey to the deadly kala azar and the death toll has risen to 31 in the last two months.
Dr Munir Lugga, director of the tropical endemic diseases in the south?s health ministry, said there has been an "unexpected" rise in victims from the fly-borne disease in the Ayod county of the troubled eastern Jonglei state.
Kala azar, or visceral leishmaniasis, is a neglected tropical disease endemic in some parts of the south that is contracted by the bite of a sand fly.
"These cases have been much earlier than normal," Lugga said, adding that 31 people died in June and July, compared to eight deaths in the previous six months.
"Accessibility to health services has also declined with the onset of the rainy season," he added.
Symptoms include fever, diarrhoea, vomiting, nosebleeds, a swollen spleen and jaundice.
Almost all untreated victims die within one to four months. However, if treatment is received on time, some 95 percent can recover.
"The ministry has enough drugs to treat all those suffering," Lugga said, adding that 118 people have been successfully treated in Ayod since December.
"However, the problem is that people in the remote areas do not have the access (to health services). Many must walk for as much as 10 hours to reach a clinic."
He also warned that the actual death toll could be higher.
"These are only the number of registered deaths," Lugga told reporters. "It is likely that there are more deaths out in the communities."
Parts of the south saw unusually heavy rains this year that caused flooding in the Jonglei state and cut off access to some areas.
There are concerns the disease could affect other remote areas, Lugga said, including counties hard hit by clashes between rival ethnic groups as well as by fighting between the military and a renegade army commander who rejected recent election results.
At least 700 people have been killed and more than 152,000 people forced from their homes across south Sudan since January, according to UN estimates.
South Sudan is still recovering from decades of war with the north, during which about two million people were killed in a conflict fuelled by religion, ethnicity, ideology and resources, including oil.
Last November the aid agency Medecins Sans Frontieres (Doctors Without Borders) launched a major campaign to tackle a "serious outbreak" of the disease.
Outbreaks occur every five to 10 years, according health experts.