Election officials' original plan of collecting preliminary results electronically was scrapped late Tuesday when only 43 percent of the 32,000 polling stations transmitted results, The Wall Street Journal reported. The number has barely moved since.
The preliminary reports from Monday's elections indicated Deputy Prime Minister Uhuru Kenyatta secured 2.8 million votes, or 53 percent, to Prime Minister Raila Odinga's 2.3 million votes, or 42 percent.
Some electoral officials drove hundreds of miles to the counting center in Nairobi to deliver paper copies of the tallies of their returns, the BBC reported.
Election officials said the computer system built to relay results broke under the volume of data transmitted. The breakdown came after electronic failures on Election Day when many of the laptop computers the election commission supplied polling places to identify voters' fingerprints malfunctioned or ran out of power, the Journal said.
Kenyatta was indicted by the International Criminal Court for his role in the violence in the aftermath of the 2007 election. In the ethnic confrontations that followed, more than 1,000 people died. Kenyatta has denied the allegations.
To avoid similar turmoil, Kenya's election commission Wednesday stepped up collection of black briefcases that contained local vote totals from each of Kenya's 47 counties.
"The country needs to know the results of these elections," said Ahmed Issack Hassan, election commission chairman.
The commission Tuesday said it tossed more than 300,000 ballots, apparently because voters put many ballots into the wrong boxes, the Journal said.
Polls indicated Odinga and Kenyatta were neck-and-neck going into Monday's election. If neither receives 50 percent of the vote, a runoff would be conducted within a month. The runoff would be delayed if a challenge to the results is sent to Kenya's Supreme Court, a prospect some analysts said was likely.
"The irregularities are certainly worthy of a court case if someone chooses to have one, and that will become more of a factor depending on how they treat the spoiled ballots," said Clare Allenson, an East Africa analyst at Eurasia Group.
The BBC said the election commission would decide whether to count the spoiled ballots after the other votes are tallied.