A security source told AFP news agency the pre-dawn raiders had fired shells at the Djibo barracks.
Burkina Faso's new self-declared military leader Captain Ibrahim Traore has accepted a conditional resignation offered by Paul-Henri Damiba to avoid further violence.
The leaders previously issued a statement to say the bloc "firmly condemns" the coup, accusing the military of forcing Kabore to resign "under threat, intimidation and pressure".
New military leader Paul-Henri Damiba promises normalcy and security to farmers and herders in Africa's Sahel nation, saying he will retake control of those areas dominated by insurgents.
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