The inflatable boat carrying 100 irregular migrants had set off at dawn from the Libyan coast, but it was intercepted by a Tunisian navy patrol boat off Zarzis, the ministry said in a statement.
The migrants, who were from sub-Saharan African nations, were in danger after the engine on the boat had broken down.
They were taken to a Tunisian maritime base at Sfax, the ministry added.
So far this year at least 453 irregular migrants have died while trying to reach Europe from North Africa, according to the International Organization for Migration.
Tunisia is a key departure point for irregular migrants attempting the dangerous crossing from the North African coast to Europe.