Health Minister Hawo Hassan Mohamed said 11 of the patients died of the disease in Sakow, while the other one died in Bu’ale, capital of middle Jubba region.
She said 43 patients are being treated at medical centers in Sakow town, and 21 in Bu’ale.
Mohamed added the government is doing its best to handle the health conditions of the patients, and will bring medical assistance to those towns as soon possible.
However, the insecurity situation in those towns might prevent health officials from providing medical assistance to those affected since the regions are currently under Al-Shabaab control.
Analysts say enhanced rainfall related to El Nino in Somalia early this year leading to some flooding and displacement of families can precipitate the outbreak of a number of diseases, including diarrhea, cholera and typhoid.
This is due to exposure to contaminated water, as well as disrupts or destroy of vital infrastructure such as health clinics, schools and roads.