National Super Alliance Presidential candidate Raila Odinga will be on the October 26 presidential ballot paper despite announcing on Tuesday that he had withdrawn from the repeat poll, the electoral commission has stated.
The IEBC added: "Once the commission receives the requisite Notice from any of the candidates, it will process the same in accordance with the requisite provision of the law".
Kenyatta, for his part, insists that the election re-run must go ahead.
Odinga contested August's election results in the country's Supreme Court.
The amendments require the approval of President Uhuru Kenyatta, whose ruling party sought the changes after the Supreme Court nullified Mr Kenyatta's election in August and ordered a new vote.
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The Independent Electoral and Boundaries Commission (IEBC) on Wednesday said that Raila had not officially pulled out of the race as he was yet to sign Form 24A as required in the electoral regulations.
Protests have been taking place nearly daily since the decision in a country that still has grim memories of post-election violence, with a disputed 2007 poll prompted politically motivated tribal clashes that left some 1,100 dead.
The opposition view is that a 2013 ruling by the Supreme Court means if any candidate withdraws, the IEBC must conduct fresh poll nominations, beginning the whole process over again.
"We have said and we continue to say that we will not participate in the elections if the environment is not conducive for a free and fair election", Odinga said. Protesters threw stones and were met with police tear gas. The outbreak of the street riots followed the publication of the decision by a Kenyan high court, according to which another candidate can be included in the list of presidential aspirants in the elections scheduled for October 26.