Colonel Mayele, commander of a tribal Mai-Mai militia, was arrested in a military operation carried out by the UN Mission for the Stabilisation of the DR Congo (MONUSCO) and the Congolese military, a UN spokesman told AFP.
"He is currently being held in Goma," the capital of Nord-Kivu province, the spokesman added, without giving more details on the arrest.
Mayele "was arrested in the Walikale region" in Nord-Kivu province in the east and was "transferred" to the Congolese military "that has opened a judicial inquiry against him," a statement from the UN said.
The UN accuses Mayele of leading a coalition of at least 200 fighters from the Mai-Mai militia and the rebel Democratic Forces for the Liberation of Rwanda who raped some 500 men, women and children.
The mass rapes took place in 13 villages in the Walikale region.
The UN expert on sexual violence in conflicts, Margot Wallstroem, who was in the region Tuesday, hailed the arrest as "a victory for justice".
"Let his apprehension be a signal to all perpetrators of sexual violence that impunity for these types of crimes is not accepted and that justice will prevail," she said.
The arrest "is a victory for justice, especially for the many women who have suffered rapes and other forms of sexual violence", she added.
Wallstroem was on her second visit to the country and criss-crossed the unstable provinces of Nord-Kivu and Sud-Kivu.
"I came to meet the victims, to hear their stories, the better to understand what is happening, their fear, their rage and their depression," Wallstroem told AFP in an interview earlier.
"I also came to get the message across that we have to pursue the perpetrators, because it's like that that you put an end to impunity."
Wallstroem visited the remote territory of Walikale in the west of Nord-Kivu, where the mass rapes took place.
"That was horror," she said. "I think that it will destroy this country, if this continues, because it will brutalise the whole society, from generation to generation, and destroy all the values, all the standards."
In Goma and in Bukavu, the capital of Sud-Kivu, as well as in the DR Congo capital Kinshasa, Wallstroem also held talks with political leaders.
The UN force has been strongly criticised for having failed to protect people in Walikale in July and August. "The means available to MONUSCO, its personnel and its capacities are not sufficient," Wallstroem said.
"We could improve the training (of UN troops), step up patrols, talk more to the population and strengthen intelligence," she said, but added that "we can't think that MONUSCO must stand in the place of the state to guarantee security."
Since the start of September, the Congolese army has led operations in the Walikale region against the FDLR and the Mai-Mai militia, who have increased their attacks against civilians in recent months.
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