The government confirmed the takeover on national TV, saying they liberated all of the places formerly occupied by the presidential guard.
Burkina Faso's army appeared to have prepared for the offensive all day, earlier surrounding the barracks, and the nearby presidential palace and national radio in the capital, Ouagadougou.
Artillery was fired at the barracks of the elite presidential guard before they took control yesterday, said army spokesman Capt Guy Herve Ye. The government did not immediately give a casualty toll.
"I call on all the elements to lower their arms and to rejoin the ranks of the army to avoid unnecessary bloodshed," Diendere said in an interview with local Radio Omega after the army attacked.
The elite presidential guard staged the coup because it was unhappy that supporters of former President Blaise Compaore, ousted in a popular uprising in October, couldn't run in elections.
The presidential guard arrested interim President Michel Kafando and interim Prime Minister Yacouba Isaac Zida on September 16.
Under a peace deal brokered last week, members of the presidential guard are supposed to disarm.
Diendere told the radio station that some 100 soldiers, a captain and an interim leader had left the presidential guard and accepted disarmament.
But the presidential guard, which initially had around 1,300 members, said yesterday that it will not give up its weapons under "shameful and violent" conditions.
"Any attempt of aggression against our regiment will result in a clear, clean and decisive response as always," the presidential guard said.
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