Low voter turnout also seen in ruling Jubilee stronghold in the Rift Valley.
Voting did not take off in the morning in some parts of Kenya as election officials failed to turn up for work over security and safety fears.
In some areas in opposition strongholds, officials could not distribute materials as youths blocked roads to prevent the election from taking place.
Opposition leader Raila Odinga called for an election boycott, urging his supporters to stay at home.
Meanwhile, President Uhuru Kenyatta and his deputy William Ruto cast their votes at polling stations in central Kenya and Rift Valley respectively.
Mr Kenyatta said as a responsible leader, he may reach out to the National Super Alliance (Nasa) leader Mr Odinga after the election as a way of unifying the country.
He acknowledged the country is grappling with tribalism, even as he reiterated that participating in an election or not is an individual’s right which must be respected.
“It’s my hope and wish that the country will move forward after this election,” he said.
Mr Ruto expressed confidence of a high voter turnout saying the Jubilee Party deserved another chance to lead the country.
He defended the move to hold the elections despite the withdrawal of Mr Odinga, the key challenger saying everyone had a constitutional right to vote or abstain.
“It is everyone right to vote or not. We are asking our supporters to come out in large number and vote for us,” he said.
Low voter turnout has so far characterised the exercise in the Rift Valley despite being one of Jubilee's strongholds.