Weapons were also seized and another militant was reportedly arrested in the raid.
The ministry said that the operation took place in the Sammama mountains, where security forces have since 2015 been battling al-Qaeda-linked militants who are based there.
In 2015, the Islamic State group claimed responsibility for three major attacks on Tunisian soil, which killed 72 people.
The most deadly of these attacks were committed at Tunis’ Bardo Museum and the seaside resort of Sousse, where 59 tourists and one Tunisian guard were killed.
Tunisia on Thursday extended a state of emergency in place since a November 2015 extremist bombing in Tunis that killed 12 presidential guards on a bus.
Defence Minister Farhat Horchani added that there had been a “major improvement” in the security situation.
“But as long as our situation is linked to Libya and as long as Libya does not have a government that is in control of the situation… the threat exists,” he said.