Authorities gave no reason for Maiga, who had been in his post since April, stepping down seven months before President Ibrahim Boubacar Keita seeks re-election.
Maiga "presented to the president his resignation along with that of the members of his government," the president's office stated, saying Keita had "accepted" his decision to quit.
The statement added a replacement prime minister and government would swiftly be found for Maiga, who had thanked the president for the opportunity to serve his country.
He was Keita's campaign director during the latter's successful run for the presidency in 2013.
He resigns with Mali's north still a theatre of unrest almost six years after a French-led military operation chased Islamic extremists linked to Al-Qaeda from a region they had taken control of in early 2012.
Mali's army, French soldiers and a UN mission (MINUSMA) still have little control over large tracts of the country, which regularly come under attack in spite of a peace accord signed with Tuareg leaders in May and June 2015 with the aim of isolating the jihadists.
The spread of the unrest this year prompted the G5 regional forum, which also includes Mauritania and Chad, to step up peace efforts with French support.
Maiga was Keita's fourth prime minister after Oumar Tatam Ly (September 2013-March 2014), Moussa Mara (April 2014- January 2015) and Modibo Keita (January 2015-April 2017).
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