The man's body was found in a house today after heavy clashes in the Sayah area near the Libyan border, a security source said.
An interior ministry spokesman confirmed that the man was killed, without providing further details.
Ten members of the security forces and one civilian were wounded in the clashes, a Ben Guerdane hospital official said. Three are still in hospital.
The army and security forces have deployed around Ben Guerdane since jihadists launched a dawn assault on security installations in the area on March 7, killing 13 members of the security forces and seven civilians.
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There was no claim of responsibility for the March 7 attacks, but authorities blamed them on the Islamic State group.
Tunisian authorities said two "terrorists" were killed Saturday in the same area.
Tunisia has failed to curb a rise in extremism since the 2011 revolution that ousted longtime dictator Zine El Abidine Ben Ali.
Last year, IS claimed attacks on the Bardo museum in Tunis and a popular resort hotel, killing 59 tourists in total, and the suicide bombing of a bus that killed 12 presidential guards.
Tunisia is tomorrow expected to host a meeting for countries neighbouring Libya, where IS has taken advantage of the turmoil after the 2011 revolution to extend its influence.