Kenya opposition presidential candidate Raila Odinga has said the electoral commission's IT system has been hacked to manipulate the election results.
He rejected provisional results from Tuesday's vote indicating a strong lead for President Uhuru Kenyatta.
But Kenya's chief electoral officer Ezra Chiloba said the systems were not compromised at any point.
The opposition's claim led to sporadic outbreaks of violence amid calls for calm from politicians.
One person was killed in a confrontation with police in the capital, Nairobi, witnesses told the BBC, although this has been denied by the government.
Police have also fired shots at opposition supporters in the western town of Kisumu, an opposition stronghold.
But Mr Chiloba said the electoral commission had received no formal complain about hacking.
Speaking on Wednesday, he added: "I wish to take this opportunity to confirm that our elections management system is secure. There were no external or internal interference to the system at any point before, during or after the voting."
Many fear a repeat of the violence after the disputed election 10 years ago. More than 1,100 Kenyans died and 600,000 were displaced following the 2007 vote.
What do provisional results say?
Raw polling data published on the website of the Independent Electoral and Boundaries Commission (IEBC) says that with 96.83% of results in, Mr Kenyatta is leading with about 54.3%, to Mr Odinga's 44.8% share of the vote.
These results mean Mr Kenyatta appears to be heading for a first-round victory. But they are not officials results, Mr Chebukati said, as Forms 34A - filled in by presiding officers to tally votes at polling stations - have not yet been checked against the results the IEBC has already declared.
The commission has not said when it will publish the final results. Legally, it has to announce the results within seven days of polling stations closing.
In order to avoid a run-off, a candidate needs 50% plus one of the votes cast and at least a 25% share of the vote in 24 of Kenya's 47 counties. There were eight candidates in all, but apart from Mr Kenyatta and Mr Odinga, none polled more than 0.3% of the vote.
Mr Kenyatta won 50.7% of the vote at the last election in 2013, narrowly avoiding a run-off.
What have observers said?
Observers from the African Union and the European Union among others issued a joint statement urging political parties "to use the legally provided channels of dispute resolution in case of any dissatisfaction with the process", adding that police should "avoid excessive use of force".
They also said the IEBC should carry out the tallying process "with full integrity and transparency".
How have Kenyans reacted?
Speaking at a press conference Mr Odinga, who heads the National Super Alliance (Nasa), said his supporters should remain calm, but added: "I don't control the people". The opposition may call for "action" at a later date, his deputy, Kalonzo Musyoka, said.
Opposition supporters have protested in the Mathare slum, one of Mr Odinga's strongholds in the capital, Nairobi.
Meanwhile, in Kisumu, a BBC reporter saw a group of several hundred of his supporters take to the streets shouting: "No Raila, no peace".
They were then dispersed by police using tear gas.
However, these appear to be isolated incidents.
Kenya's government spokesman Eric Kiraithe described them as "minor skirmishes", which the police had contained.
Internal Security Minister Fred Matiang'i urged Kenyans to continue with their normal activities but said that social media access could be restricted if it "threatens the security of the country".
What is Mr Odinga's complaint about the vote?
Mr Odinga said in a tweet that his party's own assessment put him ahead of Mr Kenyatta.
He said that the hackers had gained access to the IEBC computer system by using the identity of the commission's IT manager, Chris Msando, who was killed last month.
He alleged that the hackers had "loaded an algorithm" that allowed them to alter the results and ignore the figures being transmitted from tallying centres around the country.
Analysis: Alastair Leithead, BBC News, Nairobi
If the provisional results stand, Mr Kenyatta's winning margin of nearly 1.5 million votes should be large enough to be convincing.
This is an imperfect system - the voters' register was neither accurate nor complete, and some irregularities have been found - but not enough to account for 1.5 million votes.
The opposition is relying on a huge conspiracy to explain its margin of defeat.
So just how viable are the claims that the IEBC computer system was hacked? What's the evidence? How can it be proven or disproven?
What does the electoral commission say?
The electoral commission says it will look into Mr Odinga's claims, but urged people to wait calmly for the full results of Tuesday's vote.
"During this critical phase, we urge all Kenyans to exercise restraint as we await official results from the polling stations and indeed as they start trickling in," the commission said.
However, it admitted that a lack of mobile data coverage had delayed the delivery of the supporting documents.
There had been reports on election day of the failure of some voter-identification equipment.
Also, one in four polling stations were without strong mobile phone coverage, meaning that officials were asked to drive to the nearest town to send results.
The presidential candidates' agents would have "special access" to the forms, though, the electoral commission said.
How did the voting go?
Voting passed off largely peacefully with long queues at many polling stations, some of which remained open after the scheduled 17:00 (14:00 GMT) closing time.
But there was one heartening moment when a woman gave birth to a baby girl as she queued in West Pokot to cast her ballot. New mother Pauline Chemanang called the circumstances of the birth a "blessing" and called her baby Kura, Swahili for "ballot", according to local radio.
What is at stake?
Mr Kenyatta is hoping for a second term in office.
Voting for the national and local assemblies has also been taking place.
Mr Odinga, 72, has run for president three times and lost each time. President Kenyatta, the 55-year-old son of Kenya's founding president, narrowly beat him in the last election in 2013, but their rivalry is generations old - their fathers were political opponents in the 1960s.
Mr Kenyatta and his running-mate William Ruto were indicted by the International Criminal Court for their alleged roles in the bloodshed a decade ago. The case ultimately collapsed due to lack of evidence, and after key witnesses died or disappeared.
Kenya's election in numbers:
- Six separate ballot papers: For president, national assembly, female representatives, governors, senate and county assemblies
- 47 parliamentary seats and 16 senate seats reserved for women
- Eight presidential candidates: President Uhuru Kenyatta and opposition leader Raila Odinga are favourites
- Kenyatta beat Odinga in 2013 - their fathers were also political rivals in the 1960s
- A candidate needs 50% plus one vote for first-round victory
- More than 14,000 candidates running across the six elections
- More than 45% of registered voters under 35
- Some 180,000 security officers on duty nationwide in case of trouble