Armed officers of Mali’s anti-terror police stormed the prison to free their commander.
The exact circumstances of how Oumar Samake was released are not clear.
Some reports say prison guards stepped aside, while others say the government ordered his release to avoid unrest.
Commander Samake was accused of murder over the deaths of at least 14 anti-government protesters in July 2020.
Mali’s interim government condemned the action by “uniformed and armed men” from the Special Anti-Terrorist Forces, a statement said.
The Malian Association of Human Rights (AMDH) said it was “deeply shocked” over the incident and called it a serious attack on the rule of law.
It said officers had fired shots in the centre of the capital, Bamako, on Friday before heading to the city’s central prison, where Forsat commander Samake had been detained hours earlier.
The special forces unit has received training from both the EU and the US to help in the fight against jihadist groups which have been waging a decade-long insurgency in Mali.
The UN and France have thousands of peacekeepers based there to help tackle the jihadists.
But the unrest has left the country deeply unstable, and it has seen two military coups in the past year.