"It was a deliberate killing," said Adan Mohamed Hirsi.
The alleged shooting happened about 50km (30 miles) from Kismayo, the largest city still in militant hands.
Mr Hirsi condemned the latest killings and asked the Somali government to take action.
"This incident is very hurtful," he told the BBC's Somali service, adding that two civilians were seriously wounded.
He said that appropriate action would be taken after the investigation was completed.
Al-Shabab has been forced out of the capital, Mogadishu, and several other towns over the past year but still controls much of the countryside in south and central Somalia.
However, it still stages frequent attacks.
On Saturday, gunmen shot dead a member of Somalia's new parliament in Mogadishu.