French President Francois Hollande condemned what he called a coup in the former French colony.
Presidential forces opened fire to disperse protesters in Ouagadougou, and some were arrested, reports say.
The coup leaders have imposed a night-time curfew across Burkina Faso, and have ordered the closure of land and air borders, AFP reports.
The headquarters of Blaise Compaore’s Congress for Democracy and Progress (CDP) party were ransacked in Ouagadougou as news of the coup spread, it adds.
Francois Hollande called for the immediate release of interim President Michel Kafando and PM Isaac Zida, who were detained at a cabinet meeting in the president palace on September 16.
Their transitional government was due to hand power to a new government after elections on October 11.
Blaise Compaore was ousted in a popular uprising last year after 27 years in power, and is currently in exile.
Some of his key allies had been barred from contesting the election.
A statement issued by the coup leaders said Burkina Faso would be led by Gen. Gilbert Diendere, Blaise Compaore’s former chief-of-staff.
An earlier announcement on state television said wide-ranging talks would be held to form a new interim government that would organize “peaceful and inclusive elections”.
Transitional parliamentary speaker Cheriff Sy said the move was “clearly a coup”.
Cheriff Sy said the presidential guard had “sequestrated” the interim government, and he urged people to protest on the streets.
“We are in a resistance situation against adversity,” he added.
Earlier, there was heavy shooting by presidential forces at the capital’s Revolution Square, where protesters had gathered to demand the release of the interim leaders.
The elite presidential guard has been trained, in part, by the US. It is the most powerful armed group in Burkina Faso and often disrupted the activities of the transitional government as it tried to cling to the privileges it enjoyed under Blaise Compaore’s rule.
It is seen to be close to him, and is not popular on the streets. So its seizure of power could be a recipe for serious violence.
The transitional government might have made two mistakes – preventing politicians loyal to Blaise Compaore from running in next month’s elections and allowing the Reconciliation Commission, formed to heal wounds after the end of his authoritarian rule, to release a report calling for the presidential guard to be disbanded.
Some argue that a newly elected president would have had greater legitimacy to take such action.
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