Souleymane Diko, a local teacher, said two men on motorcycles had been reported behaving suspiciously three hours earlier.
"We now understand that they were carrying out reconnaissance on the place...," he said.
The assailants fired shots at the police station and town hall on Friday evening, bringing "terror to Boni" and leaving two people dead, one elected local official told AFP.
Boni, while actually situated near the centre of the west African nation, is part of the restive vast swathe of desert referred to as northern Mali.
While their command structure was largely smashed, Islamist fighters are still able to carry out sporadic attacks, and security in the region is further threatened by an armed separatist movement.
A Malian security source in Mopti, the nearby regional capital 460 kilometres (285 miles) northeast of Bamako, said army reinforcements had been sent to Boni.
"We don't know yet who these armed men were, but we are looking into their links with armed bandits defeated a few days ago by the Malian army at the border with Burkina Faso, almost in the same area," the source said.
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