Uganda's mililtary confirmed Wednesday that top Lord's Resistance Army rebel Dominic Ongwen was in the custody of US special forces in Central African Republic.

"His surrender puts the LRA in the most vulnerable position," army spokesman Paddy Ankunda told AFP, adding he had first surrendered to CAR's Seleka rebels, before being handed over to American forces.

But it remains unclear if US forces will now hand Ongwen over to Uganda, with the LRA commander facing crimes against humanity and war crimes charges at the International Criminal Court.

When asked if US troops would send Ongwen to Uganda, Ankunda said: "We are working out procedures."

While Uganda is a signatory to the ICC and legally bound to hand Ongwen over for trial at The Hague-based court, President Yoweri Museveni last month called for African nations to quit the ICC accusing it of being used as a "tool to target" the continent.

Ongwen is being held in the southeastern CAR town of Obo, close to the border with South Sudan and Democratic Republic of Congo, Ankunda added.

Uganda's confirmation Ongwen has surrendered follows Tuesday's announcement by the US State Department that a man claiming to be the commander was being held by American troops deployed in the hunt for rebel chief Joseph Kony.

Long driven out of Uganda, small bands of LRA fighters now roam forest regions of CAR, DR Congo, Sudan and South Sudan. Kony, who claims mystical-religious powers, has long been reported to be based in the Sudanese-controlled Kafia Kingi enclave.

Ongwen's surrender leaves rebel chief and fellow ICC indictee Kony as the last major leader still at large, Ankunda said, although the reported death of the insurgent's number two, Okot Odiahambo, has not been confirmed.

"It is only Kony left standing," Ankunda said.