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With votes from 36,125 of the 40,883 polling stations nationwide tallied, Kenyatta had 54.69 per cent of the vote, ahead of his challenger, opposition candidate Raila Odinga with 44.47 per cent, according to data released by the Electoral Commission.
Odinga rejected the early results of Tuesday's vote and said the details were "fake", because the authorities had failed to present documents verifying the results, BBC reported.
"We reject the results streamed so far," Odinga said on his Twitter account, criticising the Electoral Commission and its vote counting process.
He said that the results were "the work of a computer" and did not reflect the will of voters. "What is going on right now is a sham," he added.
Although the voting passed off peacefully without any major incidents of violence, the tension surrounding unpredictable popular reaction was still high amid fears the defeated candidate would reject the result of the election sparking popular unrest, Efe news reported.
The disputed general election in 2007 was marred by violence in which at least 1,100 Kenyans died and 600,000 were displaced.
Almost 19.6 million Kenyans went to vote in the presidential poll, resulting in large queues forming outside voting stations throughout the day.
A failure in the new biometric identification system, designed to counter electoral fraud and vote rigging, was blamed for the delays.
In 2013, Kenyatta won the presidential election with 50.07 per cent of the votes, avoiding a run-off election by just 8,000 votes.
Odinga, who garnered 43.3 per cent of the vote, filed a complaint against the election result, alleging possible irregularities. However, his complaint was later dismissed by the Supreme Court.