"The air strike occurred near Hiririo village in the Iskushuban district of Bari region this afternoon where the commander Abdihakim Dhoqob and a suspected colleague had been travelling in a car," Abdisamed Mohamed Galan said.
Speaking from the port of Bokasso, Galan did not say who had launched the strike.
The United States said Wednesday that it had resumed air strikes against al-Shabaab and has previously targeted both groups.
Muse Abdiweli, an elder in a nearby village, confirmed the attack.
"There was a heavy blast and several smaller blasts and people who went to the scene of the attack later saw a vehicle completely destroyed with human body parts shattered in pieces," he said.
Amnesty International has criticised US drone attacks and air strikes in Somalia, last month reporting that 14 civilians had been killed from only five air strikes they had examined, of a total of 110 missile blasts.
US forces said on April 5 that two civilians had died in an air strike in Somalia, the first time it has admitted non-combatant deaths since launching a wave of missiles targeting jihadist fighters.
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