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.
Cheick 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, Cheick Modibo Diarra, hereby resign with my entire government," a nervous-looking Diarra said in a short statement broadcast on state television.
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 organised crime, West African leaders have signed off on a plan to send 3300 soldiers there to revamp Mali's army and then support operations to retake the north.
Mr Diarra's forced resignation was a clear indication that those behind the coup still maintained considerable control, 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 stabilisation force," French Foreign Ministry spokesman Philippe Lalliot said.
A spokesman for the former junta said yesterday's events did not amount to a new coup and that interim civilian president Diouncounda Traore remained in place.
There was no immediate reaction from the president.