Army Chief of Staff Rachid Ammar was widely seen as having a key role in forcing out dictator Zine El Abidine Ben Ali in 2011 by not allowing troops to fire on the pro-democracy uprising.
Recently, however, Ammar has been criticized by opposition politicians for the army's inability to find a band of extremists in a mountainous area near the Algerian border.
Ammar appeared on state television late Monday to say he had submitted his resignation to President Moncef Marzouki last Saturday. He says he wanted to retire in 2006 when he turned 60 but had been persuaded to stay.