A military spokesman said Col Nyiragire "Kifaru" Kulimushi gave himself up with more than 150 of his fighters, who are also accused of mass rape.
Last month, about 100 women accused former rebels who had been integrated into the army of sexually abusing them in DR Congo's South Kivu province.
A UN envoy last year called DR Congo the "rape capital of the world".
The 16 years of unrest in eastern DR Congo have become notorious for the widespread sexual abuse of women and young girls.
Army spokesman Lt Col Vianney Kazarama told the BBC that Col Kifaru had surrendered after coming out of the bush in his eastern stronghold.
"There were 150 of them, with their weapons - including heavy weapons," he said.
Lt Col Kazarama said Col Kifaru and his men would stay at an army base, until the military and the UN officials in DR Congo conclude a joint investigations into the mass rape allegations.
The soldiers are accused of raping women and looting villages near the South Kivu town of Fizi between 10 and 12 June.
Col Kifaru had earlier deserted from a military training centre to protest against the reorganisation of the local military command.
The UN said the rapes highlighted poor discipline in the army, and the failure to properly vet rebels integrated into the army following a peace deal to end years of unrest.
Troops from Col Kifaru's group were recently convicted of raping at least 50 women in Fizi on New Year's Day.
Nine of those men, including Col Kifaru's deputy Lt Col Kibibi Mutware, were later found guilty of crimes against humanity and jailed.
Earlier this week, the UN released its findings into the mass rapes that took place last July and August when militiamen attacked villages in the Walikale area of North Kivu province within miles of a UN base.
It said the rapes of 387 people, including 44 children and 23 men, could constitute crimes against humanity.
Only one person has been indicted in connection with the case and the UN said the government needed to do more to bring the perpetrators to justice and to provide protection for victims and witnesses.
DR Congo's justice minister said he had given orders for criminal proceedings into the rapes.