Foreign Affairs CS Amina Mohamed has lost the election for African Union Commission chairperson to Chad’s Moussa Mahamat.
Amina, 56, lost to Mahamat after heads of state voted in the seventh round.
Kenya garnered 27 votes and Chad 26, while one country abstained in the fifth round In the sixth round, Chad got 28 votes and Kenya 25, while one head of state abstained.
Chad took the seventh round alone, Mahamat garnering 38 votes.
Amina and Mahamat competed against Equatorial Guinea Foreign Minister Agapito Mokuy, Senegal's Abdoulaye Bathily and Pelonomi Moitoi of Botswana.
The election took place during the 28th Ordinary Session of the Assembly of Heads of State and Government in Ethiopia's capital Addis Ababa, that will take place until Tuesday. The AU is headquartered in the capital.
Mahamat takes over from South Africa’s Dr Nkosazana Dlamini-Zuma, whose term began in 2012 and ended in June.
Amara Essy from Cote d’Ivore served as the chair from 2000 – 2003. Alpha Konare from Mali served until 2008 and Gabon’s Jean Ping until 2012.
Mahamat, born in 1960, has served since 2008. His previous posts also included a stint as prime minister.
Dlamini-Zuma's tenure had been extended by six months to give potential candidates for the position time to canvass for votes.
This was after the African leaders failed to get a two thirds majority vote for her successor in Kigali, Rwanda.
During Dlamini-Zuma's time in charge of the AU, the medical doctor has focused on reforming the AU's dysfunctional internal bureaucracy and drawing up a long-term plan for improving the lives of Africa's underprivileged citizens, especially women and children.
But she has been criticized for failing to heal the rifts created by her election and not doing more to prevent conflict in countries such as South Sudan, which the United Nations says is tilting towards genocide.
Dlamini-Zuma is now tipped as a contender to succeed her ex-husband, Jacob Zuma, as South Africa's president.
In the AUC vice chairperson vote, Ghana got 36 votes, Djibouti 14 and Libya six in the first round. In round two, Ghana acquired 44 votes emerging winner, Djibouti nine and Libya one vote. Erastus Mwencha is the outgoing VC.
Big blow to Kenya
Amina's loss is a blow to Kenya as President Uhuru Kenyatta and Deputy William Ruto has anticipated a win. At the launch of the bid, Uhuru described Amina as a focused public servant, known for the positions she has taken on issues affecting Africa and Kenya.
The government reached 51 out of 53 African Union member states and spent hundreds of millions of shillings travelling across the continent to lobby leaders to vote for Amina.
The effort that targeted all the 53 AU states had not been factored into the current financial year.
Chad, the DRC, Nigeria, Algeria, Liberia, Ghana, the Ivory Coast, Mali, Sierra Leone and Gabon are among the countries Ruto visited to lobby for the CS.
Besides Ruto, a separate seven-man Cabinet sub-committee headed by Education CS Fred Matiang’i spearheaded a separate campaign.
Members of the team included Najib Balala (Tourism), Sicily Kariuki (Public Service), Judy Wakhungu (Environment), Henry Rotich (National Treasury), Adan Mohammed (Industrialisation), Mwangi Kiunjuri (Defence) and Raychelle Omamo (Defence).
It had been said that the African leaders were receptive of Amina's candidature.
First Lady Margaret Kenyatta had praised the Cabinet Secretary for steadfastly sacrificing her life and comfort to improve conditions in Africa.
Supreme Court Judge Njoki Ndung’u said no other Foreign Affairs minister, since Independence, has faced as many challenges as Amina. She cited cases at the International Criminal Court.
Morocco re-entry, ICC among keys issues for summit
Divisive issues of Africa's relationship to the International Criminal Court and Morocco's readmission to the AU were on the agenda during the summit.
Further divisions are likely to be exposed when heads of state decide whether to approve the re-admission of Morocco.
In a race usually resolved in behind-the-scenes talks before a summit vote, three of the AU's four major regions vied for the post - the south, the east and the largely Francophone west - with some regions pushing more than one candidate.
The North African kingdom quit the AU's predecessor, the Organisation of African Unity, three decades ago amid a dispute over the body's recognition of Western Sahara, most of which has been controlled by Morocco since 1976.
But King Mohammed VI has been making diplomatic efforts over the last year to try to win Rabat's readmission.
Continental heavyweights Algeria and South Africa have been backers of the Sahrawi Republic, the domestic political movements that lays claim to the territory along the northern Sahara's Atlantic seaboard. Neither has said explicitly it will oppose Morocco's re-entry.
Preliminary meetings have also been dominated by disputes over the International Criminal Court,, which countries such as South Africa and Kenya say is a tool of Western imperialism that unfairly targets the continent.
Conversely, Nigeria, Botswana and other states say the Hague-based court is an important legal backstop for countries whose domestic justice systems have been compromised by civil conflict.
"You have all these calls for unity but actually if you look at the AU now, it is more divided than ever - over Morocco, the regional divisions and the ICC," said Liesl Louw-Vaudran, an AU expert at the Institute for Security Studies in Pretoria. "It's unprecedented."