Emmanuel Rukundo is one of two clergymen the International Criminal Tribunal for Rwanda (ICTR) indicted for their role in the 100-day slaughter in which troops and Hutu militia butchered 800,000 minority Tutsis and politically moderate Hutus.
"The Trial Chamber ... found Rukundo guilty of genocide, murder as a crime against humanity and extermination as a crime," the ICTR said in a statement.
The Arusha, Tanzania-based tribunal said Rukundo, who was often escorted by soldiers and militiamen during the violence, kept a list of local Tutsis whose movements he monitored.
As well as being involved in the abduction and murder of villagers seeking sanctuary at a seminary, it found the 50-year-old guilty of sexually assaulting a young Tutsi woman.
"The accused was found to have abused his moral authority and influence to promote the abduction and killing of Tutsi refugees," the court said.
Rukundo, a former captain in the Rwandan armed forces, was arrested in Geneva in 2001. He will receive credit for the time he has already been spent behind bars.
The tribunal began work in 1997 and has delivered 37 judgments, of which six were acquittals.
It had been meant to wind up its cases by the end of last year and then hear all appeals by the end of 2010. The U.N. General Assembly is considering whether to extend its mandate.
UN Secretary General Ban Ki-moon is visiting Tanzania and was due to tour the ICTR later Friday.