Kenyatta kept his lead in the partial results over rival Prime Minister Raila Odinga on the second day of vote counting and more than 36 hours since polls closed late on Monday.
Odinga says he was robbed of victory in 2007 when disputed results triggered bloody ethnic violence in which more than 1 100 people were killed and 600 000 were forced to flee their homes.
While millions of Kenyans turned out peacefully on Monday for the elections, how they react to the final results will be key to stability in the regional powerhouse.
Just over 40% of the almost 32 000 polling stations had sent in partial results by Wednesday morning, with so far just over five million valid votes counted from the 14.3 million registered voters.
Of those counted at 8:15 am (05:15 GMT) on Wednesday, Kenyatta had won just over 2.79-million or 53% of valid votes cast against Odinga with 2.20-million or 42%, a gap that could still be easily overturned.
But a staggering 334 000 ballots were rejected, making up some 5% of votes cast and totalling more than those so far assigned to the third candidate in the race, deputy prime minister Musalia Mudavadi, who has 2% of votes so far.
None of the other five candidates had secured more than 1% of the votes counted.
There have already been multiple complaints at the widespread failure of electronic biometric voting registration (BVR) kits introduced by the Independent Electoral and Boundaries Commission (IEBC) to frustrate potential rigging.
The BVR failure meant stations used paper records and manual registration.
The votes coming in to be tallied all but dried up overnight, with electoral officials citing technical hitches in sending results electronically.
Many returning officers were due to travel by road Wednesday to deliver them by hand.
Kenyatta's Jubilee Coalition late Tuesday called on the Independent Electoral and Boundaries Commission (IEBC) to "urgently remedy the technical issues" affecting the vote count, saying it was concerned at the slow progress.
Controversy over spoiled ballots
To win outright and avoid a second round run off, a candidate must win "more than half of all the votes cast", according to the Constitution, as well as winning at least 25% of votes in more than half of all counties.
Kenyatta's party expressed its "surprise" at suggestions it said had been made by Odinga's party to include spoiled ballots in the vote count.
If these spoiled ballots were included, it would greatly add to the numbers needed for a candidate to overcome the 50% barrier for a first round win, raising the prospect of another round due within a month after the vote.
But the Jubilee Coalition of Kenyatta and running mate William Ruto – who also faces trial later this year at the International Criminal Court (ICC) for crimes against humanity – said there was "no precedent" for including invalid votes.
Both sides expressed concern over the logistical difficulties.
Kalonzo Musyoka, Kenyan vice-president and Odinga's running mate, told reporters they were worried at the "failure of the IEBC electronic registers as well as the huge numbers of spoilt votes", but urged supporters to remain calm.
IEBC chairman Ahmed Issack Hassan said the body was investigating complaints of voting irregularities from political parties, and admitted the large number of spoilt ballots was a "concern".
"I want to assure the candidates and political parties, please don't jump to conclusions: your job is to contest the election, our job is to organise them," Hassan said.
Hours before polling stations opened on Monday, at least six policemen and six assailants – said to be members of a separatist group – were killed in clashes on the Indian Ocean coast, while one person was wounded after several bombs exploded in Mandera, on the northeastern border with war-torn Somalia.
On Tuesday, one person was wounded in a blast in a largely ethnic Somali district of Nairobi as local residents watched the vote count on television, the latest in a string of attacks there in recent months.
The results of the 2007 poll, which President Mwai Kibaki won against Odinga, sparked a wave of protests, notably over the lack of transparency in the way the votes were counted.
Odinga and his rival Kenyatta – the son of independent Kenya's founding president as well as one of Africa's richest and most powerful men – have publicly vowed there will be no repeat of the 2007-08 bloodshed.
But the trials later this year at The Hague-based ICC for Kenyatta and Ruto have raised the stakes: should they win the vote, the president and vice-president could be absent for years. – AFP