A government statement said Prime Minister Youssef Chahed had relieved Abdeljalil Ben Salem of his duties due to his "attack" on Tunisia's diplomatic principles.
On Thursday Ben Salem confirmed during a parliament session that he had "dared" to question Riyadh's ambassador to Tunis, as well as the secretary general of Arab interior ministers -- a Saudi national -- about Saudi Wahhabism being a "vehicle for terrorism".
"I say to Saudis... reform your school because terrorism has historically come from it. I say this to you with love and modesty," the minister said, according to AFP.
Ben Salem tried to row back from his comments, issuing a statement saying that Tunisia's relations with the kingdom were "completely harmonious".
Tunisia has witnessed a series of extremist attacks since the popular uprising of 2011, including deadly attacks on foreign tourists in 2015.