Malian Prime Minister Cheick Modibo Diarra has been arrested as he tried to leave the country, security sources say.
"He wanted to leave the country having incited trouble," said Bakary Mariko, a spokesperson for the group of soldiers who seized power in a March coup.
A member of Diarra's entourage told the AFP news agency that he "was arrested by about 20 soldiers who came from Kati" at a military barracks outside Bamako and headquarters of the former coup leaders late on Monday.
"They said Captain Sanogo sent them to arrest him," he added, referring to the leader of the March coup.
The source, who witnessed the arrest, said the soldiers had "smashed in the door of the prime minister's residence and took him away a bit violently".
For several weeks, tension has been mounting between the soldiers who led Mali's March 21 coup and Diarra, the civilian prime minister they were forced to appoint when they handed back power to a transitional government.
Last weekend, Diarra organised a demonstration calling for a UN resolution to back a planned military intervention to retake Mali's north from armed groups.
Diarra, a noted astrophysicist who has worked on several NASA space programmes and served as Microsoft's chairperson for Africa, had been due to leave for Paris for a medical check-up, AFP reported.
He cancelled plans to head to the airport when he learned his baggage had been taken off the plane meant to take him to France.
The source said Diarra had recorded a short message which was to be broadcast on state television, but soldiers went to the broadcaster's headquarters to confiscate the tape.
Sanogo, previously unknown, ousted President Amadou Toumani Toure's government as a rebellion by Tuareg separatists was under way in the north. The coup only made it easier for the rebels and their Islamist allies to seize control of an area larger than France.
While Sanogo handed power to a civilian government shortly thereafter, his men have remained influential in Bamako.