Kinigi wished to pursue economic development while she was prime minister, but thought that this could not be achieved until ethnic tensions between Tutsis and Hutus were reduced.

Though her government proved unable to contain the ethnic violence following the coup, she played a key role in brokering a political compromise that allowed for the election of Cyprien Ntaryamira as the next president.

[3] In 1991 she left the job[1] when President Pierre Buyoya appointed her Special Consultant in the Office of the Prime Minister,[4] making her responsible for the implementation of Burundi's structural adjustment program.

[5] The country hosted free elections, which were won by UPRONA's rival, Front pour la Démocratie au Burundi (FRODEBU).

[8] She reportedly considered the offer for some time, but eventually decided to accept it, reasoning that she was not more politically inexperienced than the army officers which had previously ruled the country.

[9] Radical UPRONA members were also displeased with her selection, since the party did not formally nominate her as a candidate, and they felt that Ndadaye had chosen her purely because she was a Tutsi woman and did not expect to rely on her abilities in office.

[5] In mid-October she dispatched her ministers across the country on a mission to promote calm and understanding; she went to the northeast to denounce the "barbarism" of political violence associated with the previous elections.

[17] Buyoya and his predecessor, Jean Baptiste Bagaza, both gave their support to her government[18] and the coup failed due to an outbreak of violence and international condemnation.

[9][a] Tutsi extremists continued to employ violence in the aftermath of the coup, intimidating Kinigi's government and hampering its ability to provide leadership to the country.

[20] Kinigi's government—comprising 15 of the original 22 ministers—stabilised the situation in Bujumbura, the capital, but proved unable to contain the ethnic violence across the country following the coup, in which thousands died.

[22] The newspaper L’Observateur argued "not having been mandated by UPRONA, knowing simply that she is Prime Minister thanks to God and to Ndadaye and to FRODEBU, the first lady [sic] will behave during the crisis of October 1993 as one would expect.

[23] On 15 November she wrote a letter to the Secretary General of the Organisation of African Unity, appealing for a military intervention to restore order in the country.

[24] In December her government appointed a commission of inquiry led by the Procurator General to investigate human rights abuses that had occurred after the coup, but its work never began due to objections from the parliamentary opposition.

[28] Ntaryamira was scheduled to be inaugurated on 22 January, but the parliamentary opposition, led by UPRONA, filed a suit with the Constitutional Court to block the installment.

[27] With the assistance of United Nations representative Ahmedou Ould-Abdallah, Kinigi brokered a compromise with the opposition,[30] whereby Ntaryamira would be installed as president with a new UPRONA prime minister,[31] and the Constitutional Court would be reinstated.

[9] Kinigi was the second woman to serve as president of an African country, after Carmen Pereira of Guinea-Bissau, who also held the office in an interim fashion.

"[33] Reflecting on her time in government in 1999, Kinigi said it made people realise "that a woman can do even more than a man can do, with a soul of a mother and strong will, at the highest level of politics.

"[26] Linking her to her contemporary in Rwanda, Agathe Uwilingiyimana, political scientist Jane Jansen wrote that the two women "owed their temporary rise to the top to an attempt to find an accommodation to the ethnic conflicts that plagued their respective countries.

She then held several international positions, including jobs at the United Nations Educational, Scientific and Cultural Organization, the United Nations Development Programme (representing it in Equatorial Guinea, Cameroon, and Senegal), and the office of the UN Special Envoy for the Great Lakes Region in Nairobi, where she served as a political advisor and programme coordinator.