The Malian army has struggled to contain the violence involving jihadists and different ethnic groups. AFP
The attack, on Saturday, took place at the Koutiala checkpoint.
"The enemies also suffered losses," the military source said, adding the situation was currently under control.
At the time of the attack, the Malian army was conducting an operation in the Koutiala area, near the border with Burkina Faso.
"The attackers, as they withdrew, took away a customs vehicle in which there was a customs officer, and six submachine guns," according to an official document detailing the attack seen by AFP.
The attack was carried out by "unidentified armed men" on motorcycles and in a pick-up vehicle, according to the same source.
Since 2012, Mali has been rocked by a jihadist insurgency led by groups linked to Al-Qaeda and the so-called Islamic State group.
The violence began in the north, and then later spread to the centre and to neighbouring Burkina Faso and Niger. Inter-communal and criminal violence is also common.
The country has been run by a military junta since August 2020, when colonels angered at failures to roll back the jihadists toppled the country's elected leader, Ibrahim Boubacar Keita.
They then staged a second de-facto coup in May 2021, but reiterated a vow to hand back control by February 2022. That timeline was recently pushed back by two years.