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Ugandan army spokesman Paddy Ankunda said Ongwen had been handed over to Ugandan troops, that are part of the AU force in CAR hunting the rebels.
He said the Ugandan commander in the AU force had "received Dominic Ongwen from US troops" at Obo, a remote town close to the border with South Sudan and Democratic Republic of Congo.
Ongwen had initially surrendered to CAR's Seleka gunmen.
Captured Lord's Resistance Army rebel chief Dominic Ongwen was handed over to African Union troops on Wednesday to be sent to trial at the International Criminal Court for crimes against humanity, Uganda's army said.
Ongwen, who surrendered last week and was in the custody of US special forces in the Central African Republic, has been sought by the ICC for almost a decade to face charges including war crimes, murder, enslavement, inhumane acts and directing attacks against civilians.
Ugandan army spokesman Paddy Ankunda said Ongwen had been handed over to Ugandan troops that are part of the AU force in CAR hunting the rebels.
He said the Ugandan commander in the AU force had "received Dominic Ongwen from US troops" at Obo, a remote town close to the border with South Sudan and the Democratic Republic of Congo. Ongwen had initially surrendered to CAR's Seleka gunmen.
"Dominic Ongwen will be flown directly to The Hague for trial by CAR authorities, he is not coming to Uganda," Ankunda added.
The handover comes a day after Uganda ended speculation that they might seek to put the former rebel on trial in a court in Kampala.
The LRA has been blamed for the slaughter of more than 100,000 people, and the kidnapping of more than 60,000 children during a three-decade-long campaign across five central African nations.
A former child soldier himself, Ongwen was a senior aide to LRA leader and warlord Joseph Kony.
Ongwen, who is in his mid-30s, is accused of directing bloody campaigns in northern Uganda in the early 2000s, where thousands of people were killed or abducted to be used as child soldiers or sex slaves.
Other abductees were deployed to carry out attacks on civilians in the Democratic Republic of Congo.
Known as the "White Ant", Ongwen's troops excelled in punishment raids, which involved slicing off the lips and ears of victims as grim calling cards.
The US State Department accused him of "murder, enslavement and cruel treatment of civilians," and offered a $5 million bounty for information leading to his capture.
Long driven out of Uganda, small bands of LRA fighters now roam forest regions of CAR, DR Congo, Sudan and South Sudan.