At least three people were killed and more than 60 injured, according to hospital sources, when members of the presidential guard fired warning shots to disperse crowds and used batons to beat back stone-throwing demonstrators.
The coup leaders' authority did not appear to extend beyond the capital and soldiers stood aside as youths demonstrated in several other cities and towns.
The protesters were demanding the release of the interim president and members of his government detained by the presidential guard on Wednesday, and the organization of elections as scheduled for Oct. 11.
The vote is meant to mark a return to democracy a year after unrest toppled President Blaise Compaore when he tried to extend his 27-year rule. The uprising became a beacon for democratic aspirations in Africa at a time when long-term rulers from Rwanda to Congo Republic are seeking to scrap term limits.
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Military stages coup in Burkina Faso
Thursday's coup drew condemnation from former colonial power France and the United States. United Nations Secretary General Ban Ki-moon also demanded the release of detained officials and resumption of the transition.
The U.N. Security Council discussed the crisis and agreed a statement calling for the release of all officials detained in the "unconstitutional and forceful seizure of power."
"The Security Council urged the perpetrators to restore constitutional order and return power to the civilian transitional authorities without delay," the council statement said.
Senegal's President Macky Sall, the current chairman of the West African ECOWAS bloc, and Benin's President Thomas Boni Yayi were to travel to Ouagadougou on Friday to act as mediators in the crisis and attempt to free the government officials.
General Gilbert Diendere, the junta leader who for three decades was Compaore's shadowy chief military adviser, said the trigger for the putsch was a proposal this week by the transitional authorities to dismantle the presidential guard.
He said the underlying cause of the military power grab was fear of instability after the transitional government barred Compaore's supporters from contesting the polls next month.
"There may be some kind of sanctions to face but we will ask the international community to be understanding of Burkina Faso," Diendere told Reuters, promising to swiftly release the president and prime minister and eventually organize elections.
Under Compaore, Burkina emerged as a regional ally of France and the United States against al Qaeda-linked militants. Burkina hosts some 200 special forces as part of France's Barkhane regional anti-terrorist operation, while Diendere took part in U.S.-sponsored regional counter-terrorism exercises in February.
UNDERLYING PRO-COMPAORE AGENDA?
In contrast to October's uprising when thousands of protesters packed the streets led by civil society groups like Balai Citoyen (Citizen's Broom), soldiers acted quickly to scatter groups of demonstrators.
The coup leaders forced private radio and television stations off the air, and journalists on the streets were threatened or beaten.
Many streets in the city center were deserted and shops were closed as sporadic gunfire rang out in several districts of the capital. Independence Square, which was the heart of October's uprising, was occupied by soldiers.
"People started to gather, then in front of us we saw a V8 (military vehicle) that drove directly into the crowd and they started shooting, killing people," said protester Bakary Zongo. "People started falling down."
In Bobo-Dioulasso, the second largest city, demonstrations continued undisturbed throughout the day and residents ignored a 7 p.m. to 6 a.m. curfew announced by the military council earlier in the day.
