The attack was on a military base in Boulkessi, according to an announcement on Malian state television late Sunday.
A resident who spoke on condition of anonymity for fear of reprisals said that Malian soldiers fled Boulkessi after the assault.
While there was no immediate claim of responsibility, suspicion fell on a group from Burkina Faso known as Ansaroul Islam, which is linked to extremist groups in northern Mali.
The group claimed responsibility for a previous attack in January that killed 11 people including soldiers in Burkina Faso.