Ntaganzwa, 58, was convicted for genocide, extermination as crime against humanity and rape as crime against humanity and sentenced him to life imprisonment, it said.
According to the statement issued by the National Public Prosecution Authority, the defendant was however"not found guilty of murder as crime against humanity and direct and public incitement to commit genocide.
The former senior local administrative official during the defeated regime before 1994 was one of Rwanda’s most wanted genocide suspects and on the list of the most wanted fugitives by the Residual International Criminal Tribunal.
He has been on trial since his deportation to Rwanda from Democratic Republic of Congo in 2016.
Ntaganzwa -- who had a $5-million (4.6-million-euro) US bounty on his head -- was accused of organising "the massacre of thousands of Tutsis at various locations," the UN-backed Mechanism for International Criminal Tribunals (MICT) said when he was arrested.
The Rwandan court found the former mayor of southern Nyakizu had personally led a series of massacres of Tutsi civilians, including an attack on a church where thousands had taken shelter.