The air strikes on the town of Jilib are understood to be part of the offensive by the 22,000-strong UN-backed AU force, who launched in March a fresh bid to wrest remaining towns from the Islamists.
“I heard two heavy explosions, military jets were flying over the city,” said Osman Mohamed, a resident of Jilib.
The impoverished town is a key Shabaab hub in southern Somalia’s Middle Juba region, some 320 kilometres (200 miles) southwest of Mogadishu.
Senior Shabaab commander Sheikh Ibrahim Abu Hamze said war planes had struck the town, but denied any casualties.
“The enemy tried to terrorise the children and women by dropping bombs in the suburbs of the city, but thanks to God, there were no casualties at all,” Abu Hamze told AFP by telephone.
“The mujahedeen fighters have managed to repel the enemy with anti-aircraft weaponry, they have fled.”
It was not immediately clear where the jets were from, but Kenya is part of the AU force and has used its air planes to strike Shabaab bases before.
Witnesses said bombs had landed on the main route out of the town.
“Two of the bombs struck the main road that goes south to Kismayu,” resident Mohamed Hashi said.
Hardline Shabaab insurgents once controlled most of southern and central Somalia.
After withdrawing from fixed positions in the capital Mogadishu nearly three years ago, they have lost most large towns to the AU and government soldiers. However, they still regularly launch guerrilla raids.