General Gilbert Diendere, who had said several times that he was willing to face justice following the September 17 putsch, was being held at the Paspanga police base yesterday near the centre of the capital Ouagadougou.
"General Diendere and his accomplices will answer for all the offences of which they are accused," the country's interim government said in a statement, adding that a "commission of inquiry" was already "hard at work" investigating the coup.
A military source said military justice would deal with Diendere.
The general, who is the former chief of staff to ousted president Blaise Compaore, had taken refuge at the residence of the Vatican's ambassador on Tuesday, just prior to an army raid on the barracks of his elite military regiment which led the coup.
They complained that pro-Compaore candidates were being barred from running in forthcoming elections.
After nearly a week of international pressure they agreed to a peace deal brokered by the ECOWAS west African regional bloc under which the interim leadership would return, and the coup plotters would stand down with their safety and that of their families guaranteed.
But tensions soared on Tuesday as some members of the RSP refused to disarm, sparking a standoff with the army at the regiment's barracks that ended with the coup plotters abandoning their base after sustaining heavy weapons fire.
Guy-Herve Kam of Balai Citoyen ("Civic Croom"), a prominent civil society group that helped sweep Compaore from power in mass protests last year, urged authorities to not only investigate crimes committed during the coup, "but all those in which the general (Diendere) could be implicated".
"This opens the way for elections to take us out of the transition," Kam added. "The resistance (to the coup) has shown a collective drive for the defence of democracy in Burkina.
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