With results in from over 40 percent of polling stations, Kenyatta has 53 percent of the vote, against 42 percent for Odinga.
Presidential candidate of the Eagle Party, Peter Kenneth has conceded defeat.
The head of the Independent Electoral and Boundaries Commission emphasised the results were provisional and urged Kenyans to wait patiently for the final outcome.
"Nobody should celebrate; nobody should complain,"he said. "We therefore continue to appeal for patience from the public, the political parties, as well as the candidates."
In 2007-8, hundreds of people were killed in post-election violence after clashes broke out when Odinga claimed he had been cheated of victory by supporters of President Mwai Kibaki.
Mr Kenyatta stands accussed of organising the 2007-8 bloodshed and is facing charges at the the International Criminal Court (ICC).
His trial starts next month.
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