President Uhuru Kenyatta last night took an early lead with more than half the votes counted, as challenger Raila Odinga disputed the results being released by the Independent Electoral and Boundaries Commission.
At around 3:00am, President Kenyatta was leading with just over six million votes to Mr Odinga's 5 million.
That totalled to some 11.4 million votes out of 19.6 million registered voters, giving Mr Kenyatta 55 per cent and Mr Odinga 44 per cent of the votes cast.
Addressing a press conference after a meeting with the electoral commissioners at the National Tallying Centre at the Bomas of Kenya, Nasa campaign managers Musalia Mudavadi and James Orengo complained that the results being released on the IEBC Online portal were a 'fraud' because they were not accompanied by copies of the original result forms from the 34 'A' and 34 'B' from the polling stations and the constituency tallying centres.
They wanted the release of the results halted until the forms were made available.
Mr Odinga also called a press conference at the Nasa offices in Westlands to reinforce the demands from his campaign managers at Bomas, saying that there was no evidence showing that the results being streamed were based on the actual count from the polling stations and the constituency tallies.
He dismissed the results as a sham, fictitious and fake.
However, the electoral commissioners had earlier addressed the press and insisted that all the results being uploaded were the exact results transmitted from the polling stations without any changes.
Earlier, the Commissioners had been holed up in a meeting with party agents at the National Tallying Centre as concerns soared over a delay in the transmission of results from the polling stations.
President Uhuru Kenyatta took an early lead with 6,331,140 votes representing 55 per cent of the 9,865,990 votes from 26, 279 of the 40,883 polling stations counted by 12.30am.
National Super Alliance's Raila Odinga was second with 5,031,737 votes representing 44 per cent of those counted.
Independent candidate Joseph Nyaga followed at a distance with 24,158 , Alliance for Real Change's Mohammed Abduba had 17,245, the Third Alliance of Kenya's Ekuru Aukot 17,022, Independent candidate Japheth Kaluyu 7,221, United Democratic Party's Cyrus Jirongo 6,940 votes and Independent candidate Michael Wainaina 5,363.
At the Bomas of Kenya, Andrew Limo, the commission's communications boss, told journalists about the meeting at the media centre at 10.30 pm.
The meeting was called to stop cases of verbal exchanges between agents and the IEBC at the national tallying centre, and worst of all on live television.
"The commission met our agents and they expressed their intention to make this a smooth process, while laying down the ground rules for how they can raise their grievances in an organised way," said Mr Muthiora Kariara, Dr Japheth Kavinga Kaluyu's running mate.
Jubilee was represented by President Uhuru Kenyatta's agent Davis Chirchir, Jubilee Secretary General Raphael Tuju and official Winnie Guchu while Nasa was represented by Musalia Mudavadi and James Orengo.
Mr Mudavadi and Mr Orengo were on phone and were overheard complaining about the apparent laxity of their agents who they accused of failing to verify that the results announced concurred with those on the forms filled at the polling stations, scanned and sent to the national tallying centre.
Mr Orengo told a group outside the boardroom after the first meeting:
"Some of the people we put here are very useless. When they were looking for jobs they were really good but now they have turned out to be a real let-down to us."
At the meeting, the commission was reported to be keen on avoiding a repeat of a similar scenario in 2013, when some agents were said to have deliberately colluded to delay the announcement of presidential election result by denouncing each and every result read out.
Since the IEBC had to resolve each dispute and try and achieve consensus on the presidential election results in 290 constituencies, the commission almost missed the seven-day window in which to declare a winner in the election.
As the commission met, concerns mounted over an apparent delay in the relaying of results, which were accessible on the commission's portals on its website and were displayed on screens at the National Tallying Centre.
By 12 am the presidential results had started trickling in as 26,279 polling stations had already posted theirs to the national tallying centre.
The electoral commission did not give an immediate explanation over the delay as even the press briefing that was scheduled for 9:30 was delayed for close to two hours.
Access to the auditorium at the Bomas of Kenya, the IEBC nerve centre, was hampered by a new requirement by the agencies handling the security of the venue that all of those accredited to enter the compound have their individual access cards activated to enter the hall.
Those managing the activation were concerned that with more than 1,000 journalists and media support staff accredited to enter the compound, the auditorium would end up being too crowded.
The journalists were joined by hordes of invited guests, such as members of the diplomatic corps and foreign observers, and many had a hard time getting into the auditorium.
The system also caused some consternation amongst the IEBC staff as their explanations that not all accredited journalists would need to be in the auditorium at the same time went unheeded.
Earlier in the day, Kenyans had turned out in millions to vote in the most competitive election which was hit by a few technical and logistical hitches.
Two people died, one on a queue waiting vote and another after casting his ballot, while a woman gave birth at a polling station.
IEBC sacked returning officers in three constituencies in Nairobi, accusing them of delaying the opening of polling stations at 6 am as scheduled. In some stations, voting was delayed for at least four hours.
President Uhuru Kenyatta of Jubilee Party and his main rival, National Super Alliance's Raila Odinga voted in Ichaweri, Gatundu South and Kibra, Nairobi respectively and declared their confidence in winning the elections, which have attracted thousands of observers.
President Kenyatta cast his vote at Mutomo Primary School before midday in the company of First Lady Margaret and said he believes he had run a campaign sufficient to convince the electorate to re-elect him.
"I feel very positive, we (Jubilee) have run a very positive campaign telling Kenyans what we have done, what we intend to do (if re-elected), and I believe Kenyans have the ability to choose and reflect on the direction that they want us to go and I believe they want us to move forward, they want us to continue living in harmony and unity and I believe they want us to have progress and I believe they will give Jubilee an opportunity to continue with the agenda that we have started for this country," President Kenyatta said.
Reported by John Ngirachu, Valentine Obara, Ibrahim Oruko, Samwel Owino, Patrick Langat and Dennis Onsongo.