The incident followed an ambush earlier Saturday on an army supply mission in the Sahel country's restive north.
"At around 1:10 pm, an attack helicopter of the Malian armed forces, returning from an operational mission, crashed in a residential area of Bamako", the General Staff of the Armed Forces said in a statement.
It cited "possible victims" without giving a number.
Mali has been battling a security crisis since jihadist and separatist insurgencies broke out in the north of the country in 2012.
A military official, speaking on condition of anonymity, said the crash occurred in the Missabougou district.
A police officer told AFP the area had been cordoned off.
"The helicopter was returning from the Mauritanian border where it had intervened against jihadists", another military source, speaking on condition of anonymity, told AFP.
The Malian army did not provide details of the operation but local officials in the town of Nara in northern Mali said an attack had taken place there on Saturday morning.
"A supply mission of the Malian Armed Forces was ambushed just 10 kilometres from Mourdiah on the road to Nara", the provincial government said, adding that no casualties had been reported yet.
On Tuesday, an official delegation was ambushed near Nara. The chief of staff of Mali's transitional president and at least two others died in the attack, which was claimed by the Al-Qaeda-linked Jama'at Nasr al-Islam wal Muslimin (JNIM).
Earlier on Saturday morning, suspected jihadists attacked a military camp in Sevare, central Mali, killing at least nine people and injuring at least 60 others, according to regional officials..
Jihadists affiliated with Al-Qaeda and the Islamic State group have escalated their operations into central Mali and neighbouring Niger and Burkina Faso.
Thousands of civilians, police and troops have been killed across the region, and more than two million have fled their homes.
The Sahel country has been ruled by the military since August 2020.
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