President Ibrahim Boubakar Keïta has been arrested by mutinying soldiers, a government spokesman has confirmed this to journalists.
Prime Minister Boubou Cissé has also been arrested, despite earlier appeals for “brotherly dialogue”.
The apparent coup attempt in the West African nation began with gunfire at a key military camp near the capital, Bamako, on Tuesday morning.
In the city, young men set a government-owned building on fire.
It comes hours after disgruntled junior officers detained commanders and took control of the Kati camp, about 15km (nine miles) from Bamako.
The mutiny has been condemned by regional group Ecowas, the African Union and former colonial power France.
Meanwhile, Nigeria and other West African nations are making progress in ensuring a peaceful resolution to the crisis in Mali with renewed emphasis on the need for dialogue.
This and other developments were the focus of a briefing by Goodluck Jonathan while meeting with President Muhammadu Buhari at the villa in Abuja.
The former president and special envoy disclosed that the judicial arm of the government in Mali has been sorted out with the reconstitution of the constitutional court and the filling of vacancies in the supreme court.
He was in the country last week for meetings with political and religious leaders, ambassadors of the United States, France, Russia, Germany and others.
On his part, President Buhari, who also visited Bamako last month, thanked his predecessor for what he calls the stamina displayed in resolving the crisis.