Interior Ministry spokesman Mohammed Ali Aroui says counterterrorist forces assaulted the house of the suspect just before midnight Saturday.
Aroui said Sunday that in the ensuing exchange of fire, Ahmed Melki known as the "Somali" was killed and three others were arrested.
Melki was wanted for involvement in several attacks, including the July 25 assassination of opposition politician Mohammed Brahmi.
Last week, Tunisian forces stormed the house of another suspected militant wanted in the February slaying of a left-wing politician.
Tunisia has been battling al-Qaida linked extremists since its 2011 revolution. AP