More than one million children under the age of five years are acutely malnourished across the country, according to the UN Office for Coordination of Humanitarian Affairs.
It says some 300,000 pregnant and lactating mothers are also affected.
In a report published on the relief web, OCHA says the situation has been driven by a number of inter-related factors.
These include rising food insecurity, high morbidity rates, limited access to safe water and sanitation, and declining availability of health services.
In its bi-weekly report, the UNOCHA says the rate of malnutrition has reached unprecedented levels mainly in the Upper Nile and Northern Bahr el Ghazal regions.
OCHA says the cases are reported mainly among children under age 5 and women, as well as other vulnerable groups, including the elderly and HIV/AIDS and TB patients.
It says Gogrial West and Renk are among the areas that have reached very high levels of acute Malnutrition.
In Western Bahr el Ghazal and the Equatoria regions, the agency says cases of acute malnutrition are also on the rise.
According to Food Security and Nutrition Monitoring System, acute malnutrition rose significantly last year compared to 2015.
The agency also says that food security in South Sudan is likely to worsen to record levels.