The country’s neighbours have blasted Friday’s alleged coup, calling it “inappropriate” for army rebels to take control when efforts were being made to impose civilian authority.
The removal of leader Lt Col Paul-Henri Damiba was deemed “unconstitutional” by regional organization Ecowas.
This is the second time this year the country’s army has seized power.
Both times, the coups’ leaders said they had to step in because national security was so dire.
Burkina Faso controls as little as 60% of its territory, experts say, and Islamist violence is worsening.
Flanked by rebel soldiers in fatigues and black facemasks, an army captain announced on national TV on Friday evening that they were kicking out junta leader Lt Col Paul-Henri Damiba, dissolving the government and suspending the constitution.
Ibrahim Traoré said Lt Col Damiba’s inability to deal with an Islamist insurgency was to blame.
“Our people have suffered enough, and are still suffering”, he said.
He also announced that borders were closed indefinitely, a nightly curfew was now in place from 21:00 to 05:00, and all political activities were suspended.
“Faced with the deteriorating situation, we tried several times to get Damiba to refocus the transition on the security question,” said the statement signed by Traoré.
“Damiba’s actions gradually convinced us that his ambitions were diverting away from what we set out to do. We decided this day to remove Damiba,” it said.
Since the takeover, there has been no word on the whereabouts of the ousted leader.
Lt Col Damiba’s junta overthrew an elected government in January citing a failure to halt Islamist attacks, and he himself told citizens “we have more than what it takes to win this war.”
But his administration has also not been able to quell the jihadist violence. Analysts told the BBC recently that Islamist insurgents were encroaching on territory, and military leaders had failed in their attempts to bring the military under a single unit of command.
On Monday, 11 soldiers were killed when they were escorting a convoy of civilian vehicles in Djibo in the north of the country.
Earlier on Friday, Lt Col Damiba urged the population to remain calm after heavy gunfire was heard in parts of the capital.
A spokesman for the ousted government, Lionel Bilgo, told AFP news agency on Friday that the “crisis” was, in essence, an army pay dispute, and that Lt Col Damiba was taking part in negotiations.
But since Friday evening Lt Col Damiba’s whereabouts are unknown. France is a traditional ally, but French diplomatic sources have told RFI radio that Lt Col Damiba is not with them nor is he under their protection.
The United States said it was “deeply concerned” by events in Burkina Faso and encouraged its citizens to limit movements in the country.
“We call for a return to calm and restraint by all actors,” a State Department spokesperson said.
The Economic Community of West African States (Ecowas) has condemned the move, stating it “reaffirms its unreserved opposition to any taking or maintaining of the power by unconstitutional means”.
In January, Lt Col Damiba ousted President Roch Kaboré, saying that he had failed to deal with growing militant Islamist violence.
But many citizens do not feel any safer and there have been protests in different parts of the country this week.
On Friday afternoon, some protesters took to the capital’s streets calling for the removal of Lt Col Damiba.
The Islamist insurgency broke out in Burkina Faso in 2015, leaving thousands dead and forcing an estimated two million people from their homes.
The country has experienced eight successful coups since independence in 1960.
