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.
Source-AFP