The crisis at the IEBC deepened on Monday when one-half of the commissioners resigned.
The three - Vice Chair Consolata Nkatha and commissioners Paul Kurgat and Margaret Mwachanya - cited bad leadership by Chairman Wafula Chebukati as their main reason.
The commission was reduced to six after Roselyn Akombe fled the country and announced her resignation from New York just before the October 26 repeat presidential election
Last week, Parliament summoned Chebukati and CEO Ezra Chiloba over the crisis after the latter was suspended ostensibly to pave way for an audit of "major procurements".
Chebukati and the two remaining commissioners can legally make operational decisions, the resignations are also a blow to the legitimacy of the commission.
The court recently ruled that amendments made to electoral laws last year were unconstitutional.
One such amendment had reduced the quorum from five commissioners to three meaning that now Chebukati aand the two remaining Commissioners cannot make any decision.
The three commissioners kept off a crisis meeting that had been called by Chebukati at the commission's offices at Anniversary Towers in Nairobi, and instead hosted the press conference for the announcement at a Nairobi hotel.
"With the deteriorating mistrust at the commission we feel that our position as commissioners is no longer tenable and we regret to tender our resignations with immediate effect," they said in a joint statement read by Mwachanya.
Their resignations follow the controversial suspension of Chiloba on April 5, a decision that split the commission down the middle.
Chiloba was sent on a compulsory three-month leave in what was the culmination of deep-seated differences between him and the Chairman.
The move left the commission divided with Nkatha, Kurgat and Mwachanya in one camp and Chebukati, Boya Molu and Abdi Guliye in the other camp.
The three faulted Chebukati for making arbitrary decisions without involving the entire commission and accused him of failing to offer a steady hand that steers the commission and instead resorting to chasing ghosts that do not exist.
"The commission's boardroom has turned into a place of money peddling, misinformation that has construed mistrust and chasing individual glory. On many instances, the Chairman has issued statements purporting to give the position of the commission but which, in the real sense, are a pure misrepresentation of facts."
Mwachanya further said they were saddened by how the Chairman resolved to suspend Chiloba without proper communication and in disregard of procedures.
"The removal of a CEO is a weighty matter that could not have been introduced as a by-the-way during the meeting. The Chairman could have waited for an appropriate time - when all the commissioners are in the country - to properly call a sitting to deliberate on the matter,' she said.
Mwachanya noted their call at the commission was to serve the country as a single unit and never 'us versus them' or 'Chair versus CEO'.
She said the functions of the commission had been crippled by the leaking of internal memos and the pursuit of self-interest.
"After the last general election, we were to take time for self-reflection and institutionalise best practices. This race to chase ghosts that do not exist must stop," she said.
The law requires the commissioners to write to the President for their resignations to take effect.
Related: CEO Chiloba suspended, IEBC in chaos