The IEBC has confirmed that 128,926 registered voters share Identification and passport numbers.
New chairman Wafula Chebukati said anomalies amounted to 0.08 per cent of the total number of voters in their database.
“The shared ID numbers could be as a result of data entry errors and forceful use of IDs to register more than once,” he told journalists in Nairobi on Tuesday.
Cord leader Raila Odinga reported double registration of his ID number after the Interior ministry said Kalonzo Musyoka lied about a similar occurrence.
Regarding the mass listing, Chebukati said 825,125 new voters have been registered countrywide since the exercise began on January 16.
The chairman noted this did not include Kilifi and Turkana countries whose data has not been tallied.
But Chebukati added: “The figures translate to 58 per cent turnout which falls below the weekly target of 1.4 million.”
He said the registration exercise has been hard hit by insecurity, drought, especially among pastoral communities and youths holed up in learning institutions.
The IEBC listed more than 80,000 voters on day one of its mass registration exercise.
CEO Ezra Chiloba said at least 2,000 people were registered in each of the 47 counties when phase two of the listing officially began.
He said the only counties whose figures had not been received were Lamu, Turkana, Tana River and Laikipia.
The commission said it will not extend the registration period and that those who will not register will be excluded from voting.
The IEBC fell short of its target of registering four million new voters in the first phase of the listing last year.
The electoral body managed to register only 1,428,056 voters, representing 34 per cent of its national target.