The Malian army had launched a surprise assault on the rebel stronghold of Kidal last Wednesday after clashes broke out in the northern town the previous weekend during a visit by Prime Minister Moussa Mara.
The failed action threatened to sink struggling peace negotiations between the government and the rebels, and plunge the West African country back into war.
The government has said that President Ibrahim Boubacar Keita did not give the order for the army's botched attempt to retake Kidal and it launched an inquiry into the matter.
"The minister of defense has resigned," his nephew Akimy Maiga told Reuters by telephone. A ministry official, who asked not to be identified, also confirmed the information.
Tuareg separatists accepted a cease-fire agreement on Friday brokered by the chairman of the African Union and U.N. special representative in Mali.
The government has accused the separatists, including the National Movement for the Liberation of Azawad (MNLA), of renewing their former alliances with al Qaeda-linked Islamist groups. Mali was plunged into chaos in 2012 after Tuareg independence fighters teamed up with armed Islamist groups to seize the north following a coup in the capital.
When they were sidelined by the better-equipped Islamists, the separatists broke with their allies. A French-led military operation routed the Islamists last year.
The MNLA says it controls at least seven northern towns in addition to Kidal and that government troops either abandoned their positions and sought refuge at the camps of the U.N. peacekeeping mission MINUSMA or fled south on Wednesday.
(Reporting by Adama Diarra; Writing by Daniel Flynn; Editing by Steve Orlofsky)
