Kenyan President Uhuru Kenyatta is leading by a significant margin as votes are counted after the election.
However the opposition, led by Raila Odinga, disputed the tally by claiming the counting process to Tuesday's election was flawed.
The website of Kenya's election commission showed Kenyatta with just over 55 percent and opposition leader Odinga with nearly 44 percent after votes were counted from more than two-thirds of the 40,833 polling stations.
However, the commission did not release information about which constituencies had been counted, so it was unclear whether Kenyatta strongholds or opposition centers had yet to be counted.
That prompted sharp criticism from Odinga, who also ran against Kenyatta in the 2013 vote and unsuccessfully challenged the results in court with allegations of vote-tampering.
The opposition figure also ran in the 2007 vote, which was followed by violence fuelled by ethnic divisions that killed more than 1,000 people.
"A clean credible process would by now have a dashboard showing all tallies from all constituencies to add to a sum total so that country can know which part of the country has been counted and what the votes are," Odinga said in a statement on Wednesday.
"The system has failed," Odinga said. He added that the election commission "has just said that no parties have disputed the results. How do parties dispute results which they do not even know their origins?"
Election officials acknowledged the opposition objection, but defended their actions.
"We believe that by displaying results, we have been doing well to enhance transparency and accountability in the electoral process, consistent with the commitment the commission has made to the Kenya people," said the vice chairwoman of the election commission.
The commission's CEO, Ezra Chiloba, also said a results screen at the commission's counting center had frozen because too much data was being received, and that tallies would be updated later Wednesday morning. . Many people are expected to vote along ethnic lines.
President Kenyatta is widely seen as the candidate of the Kikuyu people, the country's largest ethnic group, while Mr Odinga is associated with the ethnic Luo voting bloc, which has never produced a head of state.
Former US Secretary of State John Kerry, who is the chief election observer for The Carter Center, described Tuesday's vote as "an inspiring day in Kenya watching democracy in action."
"Enthusiastic voters not fazed by long lines," he tweeted.