The operations late on Saturday in Gafsa region came hours before thousands of Tunisians were expected to join world leaders including French President Francois Hollande in a march of solidarity in Tunis.
"Our forces killed nine terrorists in a large operation in Sidi Aich in Gafsa. They also captured arms and explosives," said Interior Ministry spokesman Mohamed Ali Aroui.
Two gunmen killed 21 tourists at the Bardo Museum nearly two weeks ago, in one of the worst attacks in the North African country that mostly avoided violence since its 2011 uprising against autocrat Zine El-Abidine Ben Ali.