Somali government troops backed by African Union forces on Wednesday captured the Shebab stronghold of Bardhere, one of the last key bases of the Al-Qaeda-affiliated Islamists, officials said.

"We have secured control of the town. The allied forces are now conducting mine clearing operations in the different neighbourhoods," Siyad Ahmed, a Somali military official, told AFP by telephone from the southern town.

"There was no a major resistance, and the violent elements fled when our troops approached. They have emptied the town," Ahmed said.

Witnesses in nearby villages reported heavy fighting between the Somali government and African Union troops with the Shebab, before the militants pulled out.

They also said residents of Bardhere, situated 350 kilometres (225 miles) west of the capital Mogadishu, had also fled.

A Shebab commander, Sheikh Ahmed Abu-Ubeyda, confirmed the militants had lost the town but insisted they had not been defeated and that fighting was continuing.

"The allied invading Christian forces and the Somali apostates entered parts of Bardhere this afternoon... but the Mujahedeen are putting up resistance," he said.

"The Mujahedeen fighters are still in the area and this fight will last longer than the enemy thinks," he added.

The fall of Bardhere comes less than a week after the African Union Mission in Somalia, or AMISOM, launched "Operation Jubba Corridor" -- an offensive it said as aimed at flushing the insurgents out of rural areas in southern Somalia.

The offensive has involved Ethiopian and Kenyan forces, officials said.

A statement from the Kenyan military described its capture of a key bridge near Bardhere, used by the Shebab to move its fighters and supplies within Somalia and towards Kenya, as an "operational milestone in the fight against Al-Shebab".

The Kenyan army said its troops, fighting alongside Somali soldiers, killed at least 24 Islamists in its operations. An overall casualty toll was not immediately available.

The AMISOM offensive was launched days after the Kenyan government said a US drone strike in the region killed at least 30 Shebab rebels, among them several commanders.

It also comes after last month's Shebab assault on a AMISOM base which left dozens of Burundian soldiers dead in one of the single deadliest incidents since AMISOM soldiers arrived in Somalia eight years ago.

The Shebab, meaning "youth" in Arabic, emerged out of a bitter insurgency against Ethiopia, whose troops entered Somalia in a 2006 US-backed invasion to topple the Islamic Courts Union that was then controlling the capital Mogadishu.

The loss of Bardhere will be a blow to the group, although it has bounced back from similar defeats in the past -- maintaining its capacity to conduct ambushes in rural areas as well as high-profile raids inside Mogadishu.

In a message marking Muslim Eid celebrations on Friday, Shebab leader Ahmed Diriye -- also known as Ahmed Umar Abu Ubaidah -- outlined plans for the group to increase its operations outside of Somalia and particularly in Kenya.

The group claimed responsibility for the September 2013 siege of the Westgate shopping mall in the Kenyan capital, which left 67 dead, as well as a massacre of 148 people, mostly students, at Garissa University in Kenya's northeast in April.

A string of other bombings and massacres in Kenya's northeast and along its Muslim-majority coastline have also bee claimed by the Islamists.