As of noon Friday, local time, Kenyatta had approximately 50 percent of the vote. His nearest opponent, Prime Minister Raila Odinga, had approximately 43 percent.
If either candidate fails to secure at least 50 percent of the vote, the two will face a run-off, the BBC reported.
Election officials' original plan of collecting preliminary results electronically was scrapped late Tuesday when only 43 percent of the 32,000 polling stations transmitted results.
Some electoral officials drove hundreds of miles to the counting center in Nairobi to deliver paper copies of the tallies of their returns, the BBC said.
Kenyatta was indicted by the International Criminal Court for his role in the violence in the aftermath of the 2007 election. In the ethnic confrontations that followed, more than 1,000 people died. Kenyatta has denied the allegations.
In light of the allegations, the U.S. top administration official for Africa Johnnie Carson has warned while Kenyans are free to elect who they want for president, their "choices have consequences," The New York Times reported.