"A prime minister will be named very soon and a new government will be put in place after consultations with all political forces," according to a statement from President Ibrahim Boubakar Keita’s office.
Keita accepted Soumeylou Boubeye Maiga's resignation on Thursday after lawmakers on both sides submitted a motion of no confidence against the government on Wednesday.
The move comes after violence in the Mopti region and a massacre on 23 March, where 160 people in Ogossagou, a village near the Burkina Faso border, were killed.
The Dogon people, a hunting and farming community, were accused of the murders. They have regularly quarreled with the nomadic Fulani people over land access.
The Fulani are allegedly supporting Amadou Koufa, a jihadist preacher, while the Dogon community have created self-defence groups to protect people from insurgents.
After the village massacre, however, the militia was ordered to be dissolved.
Keita went to the village after the massacre, stressing that he would reinforce security and call for justice.
But tens of thousands of Malians took to the streets of Bamako, the capital, on 5 April, protesting the violence and accusing the government of not doing enough.
Last Tuesday, Keita said in a televised address that he had “heard the anger” of the people.
The massacre was the worst since a military intervention in 2013, when French-led forces went into the Mopti area to root out Islamist extremists linked to Al-Qaeda.