The ministry said yesterday Gen Mohammed Salah Hamdi presented his letter of resignation on July 23, less than a week after 15 soldiers were killed by militants along the Algerian border.
On July 27, two other soldiers were killed by militants in the northern Kef region, also near Algeria.
Tunisia has been battling radical al-Qaida-linked Islamist militants. Their main hideouts are believed to be in the mountainous regions along the Algerian border.
Hamdi was appointed in June 2013 after the retirement of Gen Rachid Ammar, who famously refused to intervene in the popular overthrow of dictator Zine El Abidine Ben Ali in 2011.
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