Prime Minister Cheick Modibo Diarra of the transitional Malian government announced resignation and dissolved the cabinet early Tuesday, state TV reported.
Appearing on state TV, Diarra did not elaborate on reasons for his resignation.
Military sources said Diarra was arrested earlier Tuesday by troops supportive of ex-coup leader Amadou Sanogo.
The prime minister was preparing to travel to Paris late Monday for medical examination when he was detained, the sources added.
Diarra, who had been acting prime minister since April, had called for international military intervention in northern Mali being seized by rebels including both separatists and al-Qaida- linked groups.
It is unclear whether or not his resignation will affect the process of the planned military intervention in northern Mali.
The West African bloc ECOWAS, which includes Mali, produced a detailed plan last month for approval by the UN Security Council, before deploying more than 3,000 troops, probably next year, in northern Mali.
The plan is aimed at both restoring territorial integrity and constitutional rule in a country once touted as a model of democracy.
Sanogo and his supporters toppled former president Amadou Toumani Toure on March 22, citing the government's failure to curb the rebellion, which however, swept through the entire north, larger than France, in the aftermath of the coup.
Power transfer came soon after Sanogo signed an agreement with ECOWAS in April. The situation, however, remained tense with transitional President Dioncounda Traore injured by pro-junta demonstrators at the presidential palace in May.
Traore returned to his country in July after undergoing medical treatment in France for two months, during which Diarra temporarily took over his duty.
Diarra was the chief navigator of the probe "Mars Pathfinder" at NASA before becoming chairman of Microsoft Africa in 2006. He was designated as prime minister of the transitional government in April.
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