The African Union mission in Somalia said Monday its troops had killed six people in a minibus which refused to stop at a checkpoint, responding to accusations it had gunned down civilians.

In the first, Qoryoley traditional elder Mohamed Maow said AMISOM "destroyed a civilian minibus, which was carrying vegetables to Mogadishu, with a missile. All the six passengers including the driver of the minibus have died."

According to the UN mission, its troops had set up a checkpoint in the region on Saturday after they came under mortar attack and noticed "an unusual movement of vehicles ... believed to have been ferrying Al-Shabaab fighters."

"A minibus approaching the roadblock was ordered to stop but the driver defied the order and reversed the vehicle in haste, forcing our troops to shoot, killing six people in the minibus," AMISOM said in a statement.

Another elder, Moalim Ahmed Idris, said an AMISOM vehicle killed a mother and her four children in Marka.

AMISOM said that in an incident near the port city, a convoy of its vehicles was "ambushed by Al-Shabaab militants after it hit an improvised explosive device (IED).

"Our troops fought off the attackers and managed to arrest one of the fighters. By the time AMISOM left the area, no civilian casualty had occurred."

AMISOM troops were deployed to Somalia in 2007 to defend the internationally-backed government against attacks by the Al-Qaeda linked Shabaab, which regularly carries out attacks on civilian, military and government targets.

The AU has said it plans to pull its soldiers out of Somalia by 2020, however the country has yet to form an effective national army.

AMISOM has run into difficulties with its main donor the European Union cutting funding by 20 percent saying African countries must bear more of the burden of soldier salaries.

President Uhuru Kenyatta of Kenya -- which has threatened to pull out of the force over the funding cut -- on Monday urged the EU to provide more support to AMISOM.

"The region's and the world's fight against Al-Shabaab in Somalia is one of the frontlines between stability and chaotic insecurity," he said.

Meanwhile the Burundi contingent has gone unpaid for months over a spat between the AU and EU -- which wants to pay them directly to avoid money being diverted to the regime in crisis-wracked Bujumbura.