Efforts are underway to recover the body of a woman whose car was swept away by flood waters from a river, the ministry said, without specifying the location.
A 40-year-old man suffering mental health issues was found dead on Friday morning after spending the night outside in the northeastern Jendouba region, Tunisian radio station Mosaique said.
Several areas are without electricity and numerous roads are impassable in Kef, Jendouba, Siliana and Kasserine.
More than 100 people who had been stuck in their vehicles were transported to emergency lodgings, while around 100 affected by floods have been evacuated.
The country has been on alert since Wednesday due to the adverse weather.