With 87% of constituencies declared from Monday’s vote, Uhuru Kenyatta retains a significant lead over his rival Prime Minister Raila Odinga.
He has 50% of the vote, against 43.3% for Mr Odinga. A candidate needs more than 50% to avoid a run-off.
Officials had said the results would be finalised on Friday.
“There may have been errors and discrepancies here and there. Some we have already detected and we are working on them,” Kenya’s Daily Nation newspaper quotes James Oswago, chief executive of the Independent Electoral and Boundaries Commission (IEBC), as saying.
It is not clear how long the audit will take and if the results of the largely peaceful poll will still be declared on Friday evening.
Mr Kenyatta faces trial in The Hague in July for crimes against humanity.
He is accused of fuelling communal violence after the 2007 election that saw more than 1,000 people killed and 600,000 forced from their homes. He denies the accusations.
Trials at the International Criminal Court (ICC) typically last for years, but Mr Kenyatta says it would not prevent him from doing his job, if elected.
Countries including the US and UK have hinted that his election as president would have consequences for their relations with the Nairobi government – comments which have been dismissed in Nairobi as unwanted foreign interference in domestic matters.
On Friday, the ICC agreed to postpone the trial on similar charges of Mr Kenyatta’s running mate, William Ruto, by a month till May after his lawyers complained of not having enough time to prepare his defence.
Mr Oswago’s announcement came after Mr Odinga’s Cord alliance had complained that the votes from 11 constituencies were missing from the 254 officially tallied so far, the Daily Nation reports.
This meant that Mr Odinga was missing 281,611 votes compared to 25,863 for Mr Kenyatta for those constituencies, Cord said.
If the complaint is upheld it would be the latest in a series of glitches that have hit the tallying of the results.
One of these was a programming error, which led to the number of rejected votes being multiplied by a factor of eight.
This meant more than 330,000 votes – 6% – were initially rejected – enough to change the course of the election.
The electronic system was abandoned, and the process of tallying results from the country’s 32,000 polling stations was restarted by hand on Wednesday.
The number of rejected votes is now about 1% of total votes cast.
The BBC‘s Gabriel Gatehouse in Nairobi says this high-profile flop is an embarrassment to the IEBC, as well as a stain on the reputation of a country positioning itself as an African tech-hub.
The hi-tech system was introduced with one main purpose – to eliminate the possibility of vote-rigging, and give the Kenyan electorate faith in the count – but our correspondent says the failure could end up having the opposite effect.
There are fears that if the loser does not accept defeat, there could be a repeat of the violence seen after the previous poll.
The election authorities have until Monday to announce final results.
By 16:30 GMT on Friday, 254 of 290 constituencies had declared, with 10.7m ballots counted.
Mr Kenyatta, the son of Kenya’s first President Jomo Kenyatta, had 5.4m votes (50%). Mr Odinga was trailing with 4.6m (43.3%).
If no candidate gets more than 50% of the votes, a run-off will be held next month.
Both men have passed the second condition needed for victory – at least 25% of the vote in more than half of the 47 counties.
But both camps have criticised the tallying.
Mr Kenyatta’s supporters also accused the UK of meddling in the election, an allegation denied by London.