Dominic Ongwen was to be transferred to the International Criminal Court (ICC) at The Hague, said Ghislain Grezengue, the chief prosecutor in CAR.
Ongwen was under guard by United Nations forces in CAR to keep the peace after months of sectarian violence left thousands of people dead.
The International Criminal Court’s warrant of arrest for Ongwen lists seven counts, including crimes against humanity, enslavement, murder and inhumane acts of inflicting serious bodily injury.
“He should arrive in the coming days [in the Netherlands],” said ICC spokesman Fadi El Abdallah, adding Ongwen will appear before judges “within days of his arrival”.
Ongwen, a former child soldier and a long-time leader within the Lord’s Resistance Army (LRA), defected from the group in late December and handed himself over to the Seleka rebels that control swathes of north and eastern CAR. Seleka then transferred him to US forces that support a regional anti-LRA taskforce in a remote eastern part of CAR.
The rebel group is blamed for slaughtering more than 100,000 civilians since the 1980s and forcing many others into slave labour. Its leader, Joseph Kony, remains at large.
Ongwen was flown to Bangui, CAR’s capital, on Friday aboard an American plane under heavy guard by both US and Central African security personnel, said a Ugandan army spokesman.
“He belongs to ICC. Our focus now is hunting down the last man standing: Joseph Kony,” the spokesman added.
Kony is the only LRA commander still at large out of five indicted by ICC in 2005. Three have since died, the Ugandan army has said.
The LRA first emerged in northern Uganda in 1986, where it claimed to fight in the name of the Acholi tribe against the government of president Yoweri Museveni.
But over the years the LRA has moved across the porous borders of the region – it shifted from Uganda to sow terror in southern Sudan before again moving to north-east Democratic Republic of Congo, and finally crossing into south-east CAR in March, 2008.
Combining religious mysticism with an astute guerrilla mind and bloodthirsty ruthlessness, Kony has turned scores of young girls into his personal sex slaves while claiming to be fighting to impose the Bible’s Ten Commandments.
Known as the “White Ant”, Ongwen’s troops excelled in punishment raids, which involved slicing off the lips and ears of victims as calling cards.
The US State Department accused him of “murder, enslavement and cruel treatment of civilians,” and offered a $5 million (£3.3 million) bounty for information leading to his capture.
Uganda is a signatory to the ICC and is legally bound to hand over wanted suspects to the court. However, president Yoweri Museveni last month called for African nations to quit the ICC, accusing the court of being used as a “tool to target” the continent.
More than 12,000 former LRA fighters, mainly foot soldiers who were themselves abducted by the gunmen, have been pardoned under a government amnesty designed to encourage those still in the bush to surrender.