Kinshasa, DRC - A Rwandan who allegedly helped to orchestrate the 1990s genocide was sent back to his country on Sunday to be tried by a United Nations tribunal.

Ladislas Ntaganzwa was arrested in December in eastern Democratic Republic of the Congo, and has been accused of responsibility for the killing of an estimated 20,000 people. A $5m bounty was put on his head.

The extradition was an "encouraging step of regional judicial cooperation to reduce the impunity gap," said Jose Maria Aranaz, director of the UN Joint Human Rights Office in DRC.

"We expect … that his victims will be vindicated," Aranaz told Al Jazeera.

About 800,000 people, mostly ethnic Tutsis and moderate Hutus, were killed by roving Hutu militias over a 100-day period starting in April 1994, according to the UN.

Ntaganzwa was one of nine fugitives wanted for allegedly organising the mass killing.

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An extradition agreement was signed on Sunday by the Congolese justice minister and top official from the UN Mechanism for International Criminal Tribunals (MICT) in the capital, Kinshasa.

Ntaganzwa was not presented to journalists who attended the signing at the UN mission near the airport, as he stayed in a vehicle waiting to board a flight back to Rwanda.

Rwandan Justice Minister Johnston Busingye told Al Jazeera from Kinshasa the extradition was a "step in the right direction", adding he expected "justice" to prevail during the trial.

The MICT has replaced the International Criminal Tribunal for Rwanda (ICTR), which was based in Arusha, Tanzania.

Ntaganzwa was arrested in the wartorn North Kivu province by the Congolese army, according to DRC and UN officials.

However, speaking on condition of anonymity, army, police and civil society sources told Al Jazeera that Ntaganzwa was actually detained by members of the Democratic Forces for the Liberation of Rwanda (FDLR).

Some leaders of this armed group based in eastern DRC also stand accused of participating in Rwanda's genocide before fleeing the country as troops of current President Paul Kagame put an end to the massacre.

Samuel Akorimo, left, from the UN, signs an extradition order with DRC's Justice Minister Alexis Thambwe Mwamba [Habibou Bangre/Al Jazeera]

Soon after Ntaganzwa's December arrest, Congolese minister Alexis Thambwe Mwamba said he would not be sent back if Rwanda did not "reciprocate" by returning a former Congolese rebel leader who had fled there.

However, DRC reversed the decision after intense international pressure, including from UN Secretary General Ban Ki-moon, according to a senior Congolese official who also spoke on condition of anonymity, as he wasn't authorised to go on record.

"We sent him back" because he was under an international arrest warrant and DRC had to "fulfill its obligations", Thambwe Mwamba told Al Jazeera.

In the future, "if we arrest someone Rwanda wants" and that individual is not under an international arrest warrant, "we will ask for reciprocity, this is very clear", he added.

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Source: Al Jazeera