Mr Kenyatta beat then-Prime Minister Raila Odinga by 50.07% to 43.28% in the March election.
The Secretary-General later met President Mwai Kibaki and then Prime Minister Raila Odinga.
Opposition leader Raila Odinga says the presidential vote was rigged and he was robbed of victory.
His opposition rival, Raila Odinga, insists he would have won in a legitimate count.
Prime Minister Raila Odinga called it a "heinous act of aggression" during a historic exercise.
In that vote, both Mwai Kibaki, the incumbent, and challenger Raila Odinga claimed to have won.
Those elections pitted incumbent President Mwai Kibaki against Raila Odinga who leads the Orange Democratic Movement.
He is a frontrunner for the presidency, along with Prime Minister Raila Odinga, in next week's election.
BBC: ICC Kenyatta trial 'may be delayed' on defence complaint
Raila Odinga, Prime Minister of Kenya and Sukhbaataryn Batbold, Prime Minister of Mongolia.
Raila Odinga, Premier ministre du Kenya et Sukhbaataryn Batbold, premier ministre de Mongolie.
Tillman Thomas, Premier ministre de Grenade et Raila Odinga, Premier ministre du Kenya.
Kenya's new prime minister, Raila Odinga, and Mr Annan have called on the region to do more over Zimbabwe.
President Mwai Kibaki was inaugurated for a second term Sunday, but his rival Raila Odinga says the poll was rigged.
It is President Kibaki who should really pick up the phone and invite Honorable Raila Odinga to the negotiating table.
That result is likely to bring controversy in Kenya and an almost certain legal challenge from Prime Minister Raila Odinga.
In Kenya's 2007 elections, incumbent president Mwai Kibaki defeated his main rival, Raila Odinga, by a margin of 230, 000 votes.
Raila Odinga conceded gracefully despite the chants of "No Raila, No Peace" from those supporters who could not bear to lose.
Mr Kenyatta is accused of organising attacks on members of ethnic groups seen as supporting Raila Odinga against President Mwai Kibaki.
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His nearest competitor, Kenyan Prime Minister Raila Odinga, received 43.3% of the vote, according to the provisional results reported by the Kenyan broadcasters.
CNN: Reports: Kenyatta has slim majority in Kenya presidential election
In June, Kenyan Prime Minister Raila Odinga appealed to the US and EU to give financial aid for a "final onslaught" on Kismayo.
Prime Minister Raila Odinga, a presidential contender in the upcoming election, said he is against the latest bonus, which was approved Wednesday night.
In the meeting, the Kenyan side included the Right Honorable Prime Minister Raila Odinga, the Vice President, Honorable Kalonzo Musyoka, and some cabinet ministers.
WHITEHOUSE: Vice President Biden and Kenyan President Kibaki
We also congratulate the people of Kenya on the peaceful conduct of the election and commend Raila Odinga for accepting the Supreme Court's decision.
Last week's election pitched incumbent President Mwai Kibaki, a member of Kenya's largest Kikuyu tribe, against opposition leader Raila Odinga of the Luo tribe.
Negotiations between representatives of the incumbent, Mwai Kibaki, and his aggrieved challenger, Raila Odinga, continued under the aegis of Kofi Annan, a former UN secretary-general.
Prime Minister Raila Odinga and Kenyatta are the top two contenders.
"Intra-Africa trade is negligible, " Kenya's Prime Minister Raila Odinga pointed out.
Prime Minister Raila Odinga had made a promise to his constituents to build a paved bypass road that reached from one end of Kibera to the other.
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Voices elsewhere in Africa, such as those of Botswana's president, Ian Khama, and Kenya's prime minister, Raila Odinga, have become louder in calling for Mr Mugabe's demise.
In Kenya , Parliament debated amendments to the constitution that would entrench a new power-sharing arrangement agreed between the president, Mwai Kibaki, and his main rival, Raila Odinga.
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