Mali's Defence Minister Soumeylou Boubeye Maiga resigned Tuesday, a week after government troops were defeated by armed rebels in the restive northeastern town of Kidal, a presidential spokesman said.
"Mali's defence minister has offered his resignation and it has been accepted," the spokesman told Agence France Presse.
A successor would be named soon, he added.
Armed groups including the Tuareg separatist National Movement for the Liberation of Azawad (MNLA) humiliated the army in a deadly offensive across the northern desert last week which saw them seize control of Kidal, 1,500 kilometers (900 miles) northeast of Bamako.
Mali's government on Friday signed a ceasefire deal with the MNLA as well as fellow rebel groups the High Council for the Unity of Azawad (HCUC) and the Arab Movement of Azawad (MAA) after mediation by the African Union.
Kidal is the cradle of Mali's Tuareg separatist movement, which wants independence for a vast swathe of northern desert it calls "Azawad" and has launched several rebellions since the 1960s.
On Sunday Maiga said that 50 soldiers had been killed during recent fighting with the armed rebels, and another 48 wounded.
The MNLA ended a nine-month occupation of the Kidal governor's offices in November last year as one of the conditions of a June peace deal that paved the way for presidential elections.
But the process deeply divided the MNLA.
The country descended into crisis in January 2012, when the MNLA launched the latest in a string of Tuareg insurgencies in the north, which the army was ill-equipped to defend.
A subsequent coup in Bamako led to chaos, and militants linked to al-Qaida overpowered the Tuareg to seize control of Mali's northern desert.
A French-led military operation launched in January 2013 ousted the extremists, but sporadic attacks have continued and the Tuareg demand for autonomy has not been resolved.