A new “national democratic council” had taken control to end the “deviant regime”, Lt-Col Mamadou Bamba said on state television.
Interim parliament speaker Cheriff Sy said the move was “clearly a coup”.
Heavy shooting could be heard at the main square in the capital, where protesters had gathered, reports the BBC’s Yacouba Ouedraogo from the city.
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French President Francois Hollande condemned what he labelled a coup in France’s former colony.
He called for the immediate release of interim President Michel Kafando and Prime Minister Isaac Zida, who were arrested at a cabinet meeting at the president palace on Wednesday.
They were due to hand power to a new government after elections on 11 October.
Long-serving ruler Blaise Compaore was ousted in a popular uprising last year, and is currently in exile.
Some of his key allies had been barred from contesting the election.
In his announcement, Lt-Col Bamba said wide-ranging talks were being held to form a new interim government that would organise “peaceful and inclusive elections”.
The transitional speaker said the presidential guard had “sequestrated” the interim government, and urged people to protest on the streets.
“We are in a resistance situation against adversity,” he added.
A witness told Reuters news agency that more than 100 people had gathered at Revolution Square to demand the release of the interim government leaders.
Hundreds of people also protested on Wednesday to demand their release.