Sierra Leone sent 850 troops to Somalia for a 12-month deployment to fight the al-Qaeda-linked rebel group, al-Shabab, in Somalia in 2013.
Their rotation was delayed after a group of 800 soldiers, who were waiting to replace their comrades in Somalia, were quarantined after one of the soldiers was tested positive for Ebola.
"They have to go. We wish they could have stayed but they have been here long. And there is no rotation possible because of the nature of the situation," Maman Sidou, the AU's special representative for Somalia said during a farewell event for the troops held in the port city of Kismayo on Friday.
In August, Somalia's President Hassan Sheikh Mohamud said no new troops from Sierra Leone will be deployed to his country after calls by activists and a campaign on social media by Somalis calling for halt to the deployment.
"This is something that is beyond the control of Republic of Sierra Leone, beyond the control of AU and beyond the control of the Federal Republic of Somalia; but we have clearly stated that we are very grateful for their contribution. They came to Somalia at a very difficult time. They are leaving Somalia in a much, much better situation," President Hassan said during the heavily guarded farewell ceremony.
The African Union which has more than 22,000 troops in Somalia from Kenya, Ethiopia, Djibouti, Uganda, Burundi, Nigeria and Ghanan said the departing soldiers will now be replaced by other troops from countries that already have boots on the ground, until the virus has been fully contained.
The troops will withdraw from Somalia in January, Al Jazeera reported.