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The latest incident comes days after the UN Security Council and the AU established a new mission for Somalia called the African Union Transition Mission in Somalia.
The president said the decision to expel Madeira was issued by an office that didn’t have sole responsibility for making such a crucial decision. Madeira could not be immediately reached for comment.
AMISOM, whose mandate expired on Thursday, was a peace support operation with nearly 20,000 forces on the ground mainly from Kenya, Ethiopia, Uganda, Burundi, and Djibouti.
ATMIS which is multi-dimensional and under full Somalia control awaits the authorization of both the AU Peace and Security Council and the UN Security Council before taking over task from AMISOM.
The AU official has been on a three-day visit to Somalia where he held high-level engagements with government officials, civil society members, and Somalia's international partners.
The minister of foreign affairs said the Somali government will hold AMISOM leadership accountable for their illegal actions in the country.
On Saturday, an inter-ministerial meeting was held in Mogadishu in which the officials have announced they will release a formal statement in response to the bombshell report that shocked the Villa Somalia.
The AMISOM mission ends in December 2021, and the African Union is working to expand the mission's capacity and increase its troop numbers to continue operations until 2026.
Al-Shabaab claimed it has killed several African Union soldiers in the attack against the AMISOM base in the Middle Shabelle region.