An ethnic Hutu from Gitarama prefecture, Nzabonimana held the position of Minister of Planning in the MRND government of Juvénal Habyarimana from 15 January 1989 to 4 February 1991, in the successive "multi-party" government formed on 31 December 1991, and the second "multi-party" government formed on 16 April 1992.
The ICTR indictment against musician Simon Bikindi charges that Bikindi, an author of many racially charged anti-Tutsi songs, “consulted with President Juvénal Habyarimana, Minister of Youth and Sports Callixte Nzabonimana and MRND-aligned military authorities on song lyrics” before releasing them to be played on the Hutu Power radio station RTLM.
[3] After the death of Habyarimana on April 6, 1994, Nzabonimana was appointed Minister of Youth and Sports (Ministre du Sport et de la Jeunesse) in the interim government.
Between April 9 and 14 July, he is alleged to have met with fellow ministers at a number of Government meetings in which ministers received briefings on the genocide's progress, and requested weapons to distribute in their home provinces for use by the genocidaires.
According to African Rights, Nzabonimana is one of the "three key civilians" collaborating with the FLDR, operating out of the Democratic Republic of the Congo.