That's 300 million negative votes -- more than twice as many than the total number of ballots cast in the 2012 US presidential election.
Musyoka said more Kenyatta strongholds were counted Tuesday, meaning Odinga's vote total would rise as more ballots came in.
Some 58% of the 18m registered voters (out of a total population of 34m) cast their ballots, a marked rise from previous turnouts.
Perhaps 3m Zimbabweans who fled the country as refugees or economic migrants were told they could not cast postal ballots: out of a total electorate said to be 5.7m people, that is a huge share.
Late on Tuesday, the election commission announced that the spoiled ballots would count in the overall vote total, increasing the likelihood of a run-off between the top two candidates, news agencies report.
Our correspondent says the large number of spoiled ballots - about 6% of the total vote, well over double the number of votes cast for the third-placed candidate, Musailia Mudavadi - has become a major bone of contention.
When the votes were tallied by hand, the number of rejected ballots came down to about 1% of the total.
The election commission chairman announced late Tuesday that those spoiled ballots, as they are called here, will count in the overall vote total.
Late Tuesday, the election commission chairman announced that hundreds of thousands of ballots that were rejected for not following the rules would be counted in the overall vote total.
This time, with over 90% of ballots counted, he had 6.9 million votes, 51.6% of the total.
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