Fourteen suspected jihadists were killed on Friday during an "alleged escape attempt", a day after they were taken in for questioning, the Malian army said in a statement.
However, two local officials told AFP that 20 civilians had been killed or arrested in Dioura, central Mali, and cast doubt on the prison escape story.
On Tuesday Amnesty International called on authorities in Mali to investigate extrajudicial killings following the discovery last week of a mass grave containing six bodies.
Once a beacon of democracy and stability in Africa, Mali has been undermined by a coup, civil war and Islamist terrorism.
Extremists linked to Al-Qaeda took control of Mali's desert north in early 2012, but were largely driven out in a French-led military operation launched in January 2013.
In June 2015, Mali's government signed a peace agreement with some armed groups, but the jihadists remain active, and large tracts of the country remain lawless.