He has led since results started trickling in after polls closed on Monday.
Kenyatta still has over 50 percent of the vote but the gap is narrowing and has fallen to a level that could mean there is no outright winner and open the way for a tense, second round run-off against rival Prime Minister Raila Odinga (pictured).
By 5.30am GMT on Friday, with 9,325,451 total votes tallied, Mr Kenyatta had 4,701,787 votes or 50.4 percent, to Mr Odinga's 4,037,327 or 43.3 percent.
That was based on votes reported from 213 of 291 constituencies.
If no candidate achieves more than 50 percent, the top two go to a run-off tentatively set for April.
The vote has been blighted by problems, delays and technical glitches and it has emerged that a computer bug was to blame for a large number of votes being rejected.
Issack Hassan said the computer was multiplying each rejected vote by a factor of eight.
That led to disputes and allegations of fraud.
"There was an error in the way the program was written," said chairman of the Independent Electoral and Boundaries Commission (IEBC) chairman.
The poll is seen as a critical test for Kenya, whose reputation as a stable democracy was damaged by violence that followed the 2007 election.
Hundreds of people were killed in that post-election violence after clashes broke out when Mr Odinga claimed he had been cheated of victory by supporters of President Mwai Kibaki.
Mr Kenyatta stands accused of organising the bloodshed and is facing charges at the International Criminal Court (ICC).
His trial starts in July.
Image: © Getty
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