More than 10 other people were hospitalized after drinking the water in Masuubiye near the south-western city of Baidoa, regional senior official Hassan Hussein Elay said.
Elay accused the militant Islamist group al-Shabaab of poisoning the well.
‘Al-Shabaab poisoned the waterhole to prevent government soldiers from drinking water there,’ he said, without providing details.
Al-Shabaab has reportedly poisoned wells in the past. It was not immediately known if any soldiers had died in the latest incident.
There was no comment from al-Shabaab, which has fought the Somali government for a decade in an attempt to establish an Islamic fundamentalist state.