Col Goïta has now promised that a new prime minister would be appointed within days, and that elections would still go ahead next year as planned.
Meanwhile, regional leaders will on Sunday hold a “consultation” meeting in Ghana, which Col Goïta is expected to attend.
Why is Mali so unstable?
It is difficult to enact reforms quickly – and the vast landlocked country is poor, with large areas underdeveloped.
A coup in 2012 led to militant Islamists exploiting the chaos and seizing the north of the country.
French troops helped regain territory, but attacks have continued as the insurgents have capitalised on the persistent political instability in the region.
This has all led to public confidence waning over the army leaders’ ability to tackle the Islamist insurgency that has spilled into neighbouring Burkina Faso and Niger.