The new outbreak is that of vaccine-derived virus that is linked to low immunisation rates.
In June, the World Health Organization (WHO) Africa Region declared South Sudan free of the wild polio virus.
The new cases were spotted after the first sample turned positive last month.
“This polio outbreak is vaccine-derived and it is not wild polio virus. As of now, we have 15 circulating cases reported in five states,” Dr John Rumunu, a ministry official, told reporters in the capital, Juba.
The ministry has triggered a national response to the outbreak that will focus on enhancing surveillance and immunisation campaigns .
“A nationwide immunisation campaign targeting over 1.4 million children will be carried out in 45 counties in the 10 states. There will be two phases starting from first week of November,” Dr Rumunu said.