Cheikh Modibo Diarra's forced resignation at the hands of the military complicates African efforts to challenge Al-Qaeda-linked Islamists that hold the country's north.
Mali's prime minister was forced to resign on Tuesday by the soldiers who staged a coup in March, complicating international efforts to help push Islamists from the north of the country.
Once a beacon of democracy in West Africa, Mali has been mired in crisis since ethnic Tuareg rebels and Al-Qaeda-linked Islamist fighters seized the northern two-thirds of the arid nation in the wake of the coup.
Although the soldiers handed over to a civilian president and prime minister under international pressure, they have remained powerful.
Cheikh Modibo Diarra resigned as prime minister hours after he was arrested trying to leave the country for former colonial power France and was brought to the ex-junta's headquarters at a barracks in Kati, just outside Bamako.
"I, Cheikh Modibo Diarra, hereby resign with my entire government," a nervous-looking Diarra said in a short statement broadcast on state television early on Tuesday. Mr. Diarra is a former NASA scientist and Microsoft chief for Africa who was made prime minister in April.
Fearing Mali has become a safe haven for terrorism and organized crime, West African leaders have signed off on a plan to send 3,300 soldiers to Mali to revamp Mali's army and then support operations to retake the north.
Diarra's forced resignation was a clear indication that those behind the coup still maintained considerable control however, a fact that could discourage international partners from backing the plan until civilian rule is strengthened.
France called for a new government to be formed quickly after the resignation.
"These developments underline the need for the rapid deployment of an African stabilization force," French Foreign Ministry spokesman Philippe Lalliot told reporters in Paris.
A spokesman for the former junta said Tuesday's events did not amount to a new coup and that interim civilian President Diouncounda Traore remained in place.
Diarra was forced to step down during a meeting with ex-coup leader Cpt. Amadou Sanogo, according to Bakary Mariko, the spokesman.
Mr. Mariko accused Diarra of recording two speeches – the contents of which were not disclosed – and of urging his supporters to disrupt talks on the political crisis this week.
"This is not a coup. The president is still in place but the prime minister was no longer working in the interests of the country," Mariko said.
There was no immediate reaction from the president.
Downtown Bamako was calm, but the main road leading to Kati was blocked for security reasons, residents said.
Coup leader Captain Sanogo has been repeatedly accused of meddling in politics since he stepped down and was officially tasked with overseeing reforms of Mali's army.
A senior west African diplomat said Diarra's resignation shows there was a de facto leader orchestrating things in Mali.
"Sanogo is pulling at the strings. Until we have a real transitional government in place, we will keep having these problems," the diplomat said, requesting not to be named.
Even before Diarra's arrest and resignation, support for the military intervention plan was not universal.
France is keenest to see military action to tackle the Islamist groups, including al-Qaeda's North African wing, AQIM. But the United States and the United Nations have expressed concern, saying the plan lacks necessary detail.
The United States warned on Monday that Mali was "one of the potentially most explosive corners of the world".
Some of Mali's politicians support the idea of a foreign-backed military operation while others, including much of the military, say they need only financial and logistical support.
Mariko said the Malian army was ready to act even without international help.
"We want the help of the international community but if it has to wait until September or until an undefined date, then the Malian army will act to free its territory," he said.
Diarra was made prime minister when the junta officially handed power back to civilians. As the son-in-law of Moussa Traore, a former Malian coup leader and president, he appeared to have good ties with the military.
However, tensions became particularly acute in recent weeks, with analysts saying Diarra, a relative newcomer to Malian politics after years abroad, seemed keen to establish a political base of his own ahead of any future elections.
Mariko later told French television France 24 that the prime minister had failed in the two missions of liberating the north and the organizing free and transparent elections.
"Since he was appointed he has not acted as a man of duty. Everything he did was for his own personal agenda," he said.