Jean-Bosco Uwinkindi is accused of inciting and directing dozens of attackers to kill Tutsis during the 100-day genocide that began in April 1994. At least 500,000 members of the Tutsi ethnic minority and moderates from the Hutu majority were slaughtered.
Survivors of the attacks were brought to Uwinkindi's church to be killed, according to the indictment against him at the U.N. International Criminal Tribunal for Rwanda. About 2,000 bodies were found near the church when Uwinkindi fled Rwanda in July 1994, it said.
There was a $5 million reward for Uwinkindi's arrest. Uganda police spokeswoman Judith Nabakooba said that he was arrested Wednesday following a tip from government intelligence.
Uwinkindi, a Pentecostal pastor, was one of nearly a dozen suspects who remain at large 16 years after the genocide.
Police said arrangements were being made to transfer him to the international tribunal, located in Arusha, Tanzania.
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