President Ibrahim Boubacar Keita accepted the resignation on Thursday without giving a reason for the departure of Prime Minister Soumeylou Boubeye Maiga.
“A prime minister will be named very soon and a new government will be put in place after consultations with all political forces” from both the ruling and opposition sides, the statement from Keita’s office said.
The president had on Tuesday said in a televised address that he had “heard the anger”, without explicitly naming the prime minister.
Legislators had discussed a possible motion of no confidence in the government because of the massacre and failure to disarm armed groups or beat back fighters.
The March 23 killings by suspected hunters from the Dogon community on Ogossagou, a village in central Mali populated by rival Fulani herders, were bloody even by the recent standards of Mali’s ever-worsening violence.
They followed a deadly assault by armed fighters on an army post that killed at least 23 soldiers, also in Mali’s central region, which was claimed by an al-Qaeda affiliate that counts many Fulani herders in its ranks.
Malian authorities have detained five people suspected of taking part in the massacre. But they have not yet succeeded in disarming the group that many believe organised it, despite pledges by Maiga and Keita to do so.
The killings in Ogossagou, which left the charred bodies of women and children smouldering in their homes, shocked a population that has grown increasingly frustrated by the failure of government forces to protect them from both armed-group onslaughts and ethnic reprisals.
Critics argue that the Malian leader has not done enough to prevent intercommunal violence.
“There is clearly dissatisfaction with the security situation in the country,” Al Jazeera’s Nicolas Haque, reporting from neighbouring Senegal, said.
“At the same time, the lives of ordinary people in Mali are getting worse. The price of basic necessities like water, electricity and food has risen by 20 percent in the last year. The PM was elected in August with a promise for change but many Malians are not seeing that change.”
Earlier this month, demonstrators called for him to “get out” of office, with some holding signs demanding the withdrawal of the United Nations peacekeeping mission in the country, MINUSMA.
The United Nations has more than 16,000 personnel on the ground in Mali, including a contingent of 12,418 troops made up of forces from countries including Burkina Faso, Senegal, Niger, Togo and Chad.
“Our children, our husbands and our parents are dying because of the bad government of IBK and his clan,” Mariam Fomba, the widow of a soldier, told AFP news agency at the protest in Bamako.
“Enough is enough, we cannot continue with this regime,” said Fomba.