Mali President Ibrahim Boubacar Keita was arrested on Tuesday by mutinying soldiers in the capital Bamako, two security sources told the Media.
Their actions began with gunfire inside a key military base, some 15km (nine miles) from the capital, Bamako, on Tuesday morning.
In the centre of Bamako, young men looted a government-owned building and set it on fire.
The mutiny has been condemned by regional group Ecowas and former colonial power France.
The unrest coincides with calls for more protests to demand that the president resign.
Mr Keita won a second term in elections in 2018, but there is widespread anger over corruption, the mismanagement of the economy and the worsening security situation with jihadist and communal violence on the increase.
A spokesman for Keita could not be reached for comment.