"The commission in its current state can surely not guarantee a credible election on 26 October 2017. I do not want to be party to such a mockery to electoral integrity," Roselyn Akombe wrote in the statement from New York.
The resignation of one of the country's top poll officials is the latest dramatic twist in an election process that has plunged the East African nation into crisis.
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The country's Supreme Court on September 1 ordered the Independent Electoral and Boundaries Commission (IEBC) to carry out a re-run of the presidential election, after annulling the vote due to "irregularities" and mismanagement by officials.
Divisions in the commission burst into the open days later when a letter was leaked from the panel's chairman to its CEO questioning a host of failings in the conduct of the August 8 poll.
Akombe said that she had questioned her role at the commission for many months, but had "soldiered on".
"Sometimes, you walk away, especially when potentially lives are at stake. The commission has become a party to the current crisis. The commission is under siege," she wrote.