The rebel surrender follows a crushing defeat at the hands of the UN-backed Congolese armed forces.
"He is with our forces, yes, Makenga has crossed into Uganda," a senior Ugandan military officer told AFP, although he declined to clarify if he had formally surrendered or was under arrest.
Paddy Ankunda, a colonel in the Ugandan army, told AFP that 1,500 men from the M23 -- a number thought to account for more or less the entire force -- had crossed into Uganda and given themselves up, and were now being held in the Kisoro border district.
However, Ankunda said he was "not aware" if Makenga was among those to have surrendered.
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Uganda has been accused by United Nations experts of backing the M23, claims Kampala has strongly denied.
The rebels' surrender puts paid to fears that they might try to fight on despite having been outweighed by superior firepower, notably helicopter gunships.
Makenga, 39, a former colonel in the DR Congo army, is accused of masterminding killings, abductions, using rape as a weapon of war and recruiting child soldiers, and is on both UN and US sanctions lists.