Witnesses earlier had told a UN tribunal that the ex-higher education minister Jean de Dieu Kamuhanda handed out guns, grenades and machetes and personally led attacks on civilians by soldiers and militia.
"Kamuhanda was found guilty of genocide and was sentenced to spend the rest of his life in jail," a spokesman for the International Criminal Tribunal for Rwanda (ICTR), Bocar Sy said.
The ICTR is trying the perpetrators of the tiny central African country's 1994 genocide, in which extremists from the ethnic Hutu majority killed minority Tutsis and politically moderate Hutus during a 100-day orgy of violence.
Witnesses also narrated how Kamuhanda led an attack on a parish church where refugees were sheltering.
"The chamber finds that the high position Kamuhanda held as a civil servant can be considered as an aggravating factor," Judge William Hussein Sekule said.
"He instigated and led an attack to kill people who had taken shelter in a place universally recognized to be a sanctuary. As a result of this attack many people were massacred."
Kamuhanda was arrested in France in November 1999 and transferred to the ICTR where his trial began in September 2001.
The UN court, set up in November 1994, has now sentenced 17 people.