A statement from President Ibrahim Boubacar Keita's office said he had accepted Soumeylou Boubeye Maiga's resignation and that of his government two weeks after mass protests erupted over the rising tide of violence.
The discovery of the bodies was another reminder of the task facing President Andres Manuel Lopez Obrador, who took office in December vowing to reduce the gang-fuelled violence.
The gunmen attacked the villages of Sagho and Toekodogo, in the Barsalogho district, on Saturday, Defence Minister Cheriff Sy said in a statement, describing them as members of "armed terrorist groups".
The crash occurred in a remote, hilly area of the north-central state of Queretaro on Friday. The MI-17 helicopter, which took off from Valle Verde in the neighbouring state of San Luis Potosi.
One attack on the main street of Tunis wounded three civilians and two police personnel, the interior ministry initially said.
"Some bodies were visible during the helicopter recce. They were on the same route as the climbers had taken," the source said, requesting anonymity.
The Taliban claimed responsibility for detonating the bomb near the National Directorate of Security (NDS) compound in Ghazni city during Sunday morning's rush hour.
Dissident republican group the New IRA on Tuesday admitted responsibility for killing Northern Irish journalist Lyra McKeen during rioting in Londonderry last week, in a statement to The Irish News.
The plane crashed near the town of Dixon Cove, a few minutes after taking off from the island's airport, rescuers said.