Elie Ndayambaje was born on 8 March 1958 in Cyumba in the commune of Kibayi, Butare prefecture, Rwanda. He was the mayor of Muganza commune in Butare prefecture from 1983 to 1992, and again from 22 June until July 1994, at which date he fled Rwanda. In this capacity he was the representative of the executive power at the communal level. He exercised authority over his subordinates and could requisition the communal police. Even during the period when he was no longer de jure mayor, he continued to exercise his authority over his former subordinates.
From end 1990 until July 1994, Ndayambaje was said to have adhered to, and participated in the detailed development of a plan aimed at exterminating the Tutsis. Amongst other elements, this plan included recourse to hatred and ethnic violence, the training of and distribution of arms to militias as well as the drafting of lists of people to be eliminated. In the accomplishment of this plan, he is accused of having planned, ordered and participated in the massacres. From April to July 1994, Ndayambaje was said to have publicly incited the population to exterminate the Tutsi population.
Before and during the 1994 killings in Butare, Ndayambaje reportedly distributed weapons to the militiamen and to certain civilians with the aim of exterminating the Tutsi population and the moderate Hutus.
On 20 April 1994, Ndayambaje was alleged to have led the police forces to Gisagara where they joined the military in arresting refugees and taking them to the nearby hillside of Kabuye. They are then said to have separated the Tutsis from the other refugees and to have forced them to hand over their traditional tools. On 22 April 1994, Ndayambaje, accompanied by the communal police, gendarmerie, military and armed civilians, reportedly attacked these refugees. Numerous Tutsis were killed or wounded. During the following night, they surrounded the survivors in order to prevent them from escaping. On 23 and 24 April, the attacks against the refugees in Kabuye continued with Ndayambaje reportedly transporting the attackers to the site and furnishing them with weapons. Furthermore, Ndayambaje himself was reported to have thrown hand grenades into the crowd of refugees.
Between April and June 1994, Ndayambaje was said to have lent assistance to Alphonse Nteziryayo (Director of Civil Defence of Butare prefecture) fby supervising the training of the militiamen and in the distribution of arms to them.
In early July 1994, in the face of the advancing FPR (Front Patriotique Rwandais, an opposition group consisting mainly of Tutsi refugees and led by Paul Kagame), Ndayambaje fled Rwanda. On 28 June 1995, he was arrested in Belgium.