Seifeddine Jameli, as known as Abou al-Qaaqaa, belonged to the Tunisian branch of the Islamic State (IS) group, Jund al-Khilafa (the soldiers of the caliphate), the ministry said in a statement.
He was killed overnight by special forces in the central region of Mount Mghilla, it said, adding that weapons were seized during the operation.
Since its 2011 revolution, Tunisia has been hit by an upsurge in jihadist violence in which dozens of police, soldiers and civilians have been killed.
The beheading of a teenage shepherd by jihadists as his sheep grazed on Mount Mghilla last November also horrified the country.