This same group in May invaded the presidential palace, as soldiers looked on, and beat the country's interim president Dioncounda Traore, until he lost consciousness. That incident brought the international community down like a hammer on the head of Mali's junta.
Sanogo signed a lengthy accord, agreeing to step down, and retreated from public life, although there were signs that the military still called the shots in Bamako.
Junta spokesman Bakary Mariko acknowledged that soldiers allied with Sanogo arrested the prime minister, and are now holding him under house arrest. Mariko said that Diarra was "not getting along" with either the interim president, or the coup leader Sanogo.
"He says he's going to Paris for medical tests ... but we know better and realize that he is trying to flee in order to go and create a blockage in the Mali situation ....It's the reason why Mali's army has taken things into their own hands and told Cheikh Modibo Diarra to resign for the good of Mali," Mariko said.
Human Rights Watch's senior researcher for West Africa, Corinne Dufka, condemned the military's intervention, saying it fits with the pattern of abuse by the soldiers ever since the coup eight months ago.
"They've arrested, beaten and intimidated journalists; tortured and disappeared military rivals; and now, apparently, arbitrarily detained the prime minister. None of these incidents have been investigated and those responsible appear to have been emboldened by the shameful lack of accountability," said Dufka.
Diarra, an astrophysicist who previously led one of NASA's Mars exploration education programs, was initially seen as in-step with Sanogo. Critics lambasted him for frequently driving to the Kati barracks to see the coup leader, long after Sanogo was supposed to have handed power to civilians. In recent weeks though, Diarra has taken stances that sometimes conflict with Sanogo.
Bamako remained calm on Tuesday, as the capital awoke to what some are calling a "mini-coup." People went about their daily lives, but with a sense of deep disappointment in this nation once held up as a model democracy in Africa.
Aboubacrine Assadek Ag Hamahady, a professor at Bamako's university said: "I really am struggling to understand — so if the prime minister is not doing his job properly, it's up to the junta to come and arrests him? So what's the purpose of having a President? ... Based on what law, on what legal text can the junta justify this arrest?"
Callimachi reported from Dakar, Senegal. AP writers Geir Moulson in Berlin, Don Melvin in Brussels and Jamey Keaton in Paris contributed to this report.
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