AU chief Nkosazana Dlamini-Zuma ordered an investigation after the AU mission in Somalia (AMISOM) was accused of raping women in a damning Human Rights Watch report last month.
A team is "to conduct investigations into the specific allegations of sexual exploitation and abuse made against AMISOM personnel, particularly the Ugandan and Burundian contingents," the AU said in a statement.
The 22,000-strong AMISOM force, with soldiers drawn from six nations, have been fighting alongside government troops against the Al-Qaeda-linked Shebab insurgents since 2007.
They "will be responsive to the needs of alleged victims and potential witnesses as well as to the wishes of all concerned to find out the truth about these allegations," AMISOM said in a statement.
The AU force AMISOM said HRW's allegations were "isolated" incidents and called the report "unbalanced and unfair".
Several of the women mentioned the HRW report described how they had gone to the AU camp seeking medicine for their sick babies, but where then forced to have sex.
The vulnerable women largely came from camps in the capital Mogadishu, having fled rural Somalia during a devastating famine in 2011.
"The findings and recommendations will be made public... with due regard to victim protection, the rights of alleged perpetrators as well as the operational imperatives of AMISOM," the AU statement added.
AMISOM donors include the United Nations, European Union, Britain and the United States.
Conditions in Somalia remain dire, with the United Nations and aid workers warning that large areas are struggling with extreme hunger, three years after famine killed more than a quarter of a million people.
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