African Union Commission chief Moussa Faki Mahamat. AFP
"He strongly condemns the attempted coup d'etat against the democratically elected president," the AU said in a statement.
"He calls on the national army and the country's security forces to strictly adhere to their republican vocation, namely the defence of the country's internal and external security."
President Roch Marc Christian Kabore was reportedly held by soldiers on Monday along with members of his cabinet after troops rose up at several army bases across the West African state on Sunday.
Soldiers had demanded the sacking of the military top brass and more resources to fight the Islamist insurgency that erupted in 2015.
Faki called on troops to ensure the "physical integrity" of the president and his detained ministers, and urged for the crisis to be resolved through dialogue.
The West African regional grouping ECOWAS on Monday also said it held the soldiers responsible for the wellbeing of the president following what it also described as a "coup attempt".
Mobile internet has been cut since Sunday in the capital Ouagadougou, making it difficult to verify the situation on the ground.t since Sunday in the capital Ouagadougou, making it difficult to verify the situation on the ground.