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Nizeyimana will be flown to Arusha, Tanzania, where the International Criminal Tribunal for Rwanda sits.
More than half a million members of the Tutsi ethnic minority and moderates from the Hutu majority were slaughtered during the 100-day Rwandan genocide in 1994.
Rwanda's genocide began hours after a plane carrying President Juvenal Habyarimana was shot down.
The former captain in Rwanda's army is wanted on charges of genocide by the tribunal. Under the U.S. State Department's Rewards for Justice program, there is a reward of up to $5 million on Nizeyimana's head for any information leading to his capture.
According to a 2000 indictment prepared by the tribunal, Nizeyimana is alleged to have formed secret units of soldiers that carried out the execution of the then Queen of Rwanda, Rosalie Gicanda, a symbolic figure for all Tutsis, among other prominent Tutsis.
Nizeyimana is the second high-profile arrest of a key Rwanda genocide suspect in two months.
A former mayor, Gregoire Ndahimana, appeared before the tribunal last week after being captured in Congo in August. Ndahimana had been on the run for 15 years and had a similar bounty on his head, but no one claimed it when he was arrested.
With Nizeyimana's arrest, 11 top suspects remain with similar bounties on their heads for their alleged roles in the 1994 genocide.
