There was confusion at the Bomas of Kenya on Monday after the IEBC revoked the certificate of Umoja Summit presidential hopeful Walter Mong'are.
IEBC chairman Wafula Chebukati said he was forced to revoke the certificate after "new information emerged".
Chebukati had last week on Monday cleared Mong'are as "having complied with all the regulations".
The deadline for the clearance of presidential candidates is Tuesday.
The revocation might raise suspicions on the validity of the whole process and the commission's ability to deliver a credible poll.
Chebukati has been turning away hopefuls who failed to present the required documents.
The revocation of Mong'are's certificate happened moments after Safina party candidate Jimmy Wanjigi and running mate Willis Otieno accused the commission of applying double standards in the process. They were disqualified over lack of a degree.
"You have already set precedence by clearing the first presidential candidate with the same degree issue," Otieno said.
Chebukati also cited failure to meet the requisite signatures and failure to submit copies of IDs of supporters who endorsed his presidential bid.
"We have allowed others who have problems with signatures to harmonise and we can also allow you in the remaining hours to do so," he told Wanjigi when he appeared at 11am. He was also accompanied by his wife, Irene Nzisa.
As Wanjigi left the venue maintaining he would be on the ballot, Chebukati and other commissioners went to a private meeting.
It is at this meeting that Chebukati decided to summon Mong'are.
Chebukati said upon verification of his documents, it became apparent that he was not qualified. The information, he said, was not available to the returning officer on the day he was cleared.
"Upon emergence of some new information and upon verification, it became clear he lacked academic qualifications and so we had to revoke his clearance certificate," he said.
Mong'are could not be reached for comment over the latest development
Defending his decision, Chebukati cited Section 42 (2) (c) on the general regulations of the election law in which he said the returning officer may revoke a nomination certificate on grounds that a candidate is not qualified.
Chebukati also released the names of four candidates he said had satisfied the commission with all the necessary requirements.
They are Deputy President William Ruto (UDA), Raila Odinga (Azimio la Umoja One Kenya Alliance), George Wajackoyah (Roots Party) and David Wahiga of Agano party.
This has deemed the hopes of all independent candidates who were eyeing the seat.
Averting what would have been the longest presidential ballot paper in the country's polls, the IEBC trimmed the list by rejecting applications of all the nine independent aspirants.
The nine, alongside other three from political parties, failed to pass the test to make it to the ballot.
Those who appeared but failed to submit the requisite documents, including a sufficient list of supporters and academic qualifications, are Gibson Ngaruiya, Dorothy Kemunto, James Kamau, Jeremiah Nyaga, Jane Juliet Munyeki, Peter Kingori, George Munyotta and Muthiora Kiriara.
Muthiora burnt his voter's card in front of Chebukati after being denied clearance to vie.
Edited by A.N