The seizure of power by some military leaders on Friday marked Burkina Faso's second coup this year.
A day after junior military officers toppled Burkina Faso's junta leader Paul Henri Damiba, the army issued a statement, dismissing the "coup" claim by the officers as an "internal crisis" within the military.
The weekend has been intense for the western African nation where a raging militancy has become a headache for successive regimes.
In January this year, lieutenant colonel Damiba deposed the elected President Roch Marc Christian Kabore in a coup, which followed heavy casualties suffered by poorly equipped soldiers in militant attacks.
Later, Damiba agreed to a democratic transition with the 15-member Economic Community of West African States (ECOWAS). Under a deal, the constitutional order was supposed to be restored by July 2024.
But on Friday soldiers led by 34-year-old Captain Ibrahim Traore said they have taken over the government.
Earlier on Saturday, Traore's men alleged that Damiba was hiding at a French military base and planning a counteroffensive from there.
Hours later, the military's statement came out.
"Following an internal crisis within the national armed forces, a few units have taken control of some arteries of the city of Ouagadougou, demanding the departure of Lieutenant-Colonel Damiba. Dialogue is ongoing," the army's general staff said in a statement.
France, the former colonial power in Burkina Faso, has denied any involvement.
Meanwhile, there were reports of a fire breaking out at the French embassy in the capital.
Damiba accused of failure
On Friday, more than a dozen soldiers in fatigues appeared on Burkina Faso's state television and radio broadcaster to announce the removal of Damiba.
"We have decided to take our responsibilities, driven by a single ideal: the restoration of security and integrity of our territory," they said.
The African Union, the European Union and US have all condemned the latest coup, saying it will hamper efforts to revive democracy.