The three commissioners said Monday that the vote to suspend CEO Ezra Chiloba was not done properly.
Magaya claimed that the three commissioners who resigned on Tuesday; Consolata Maina, Margaret Mwachanya and Paul Kurgat were part of a Ruto wing at the commission that was acting on the DP's instructions.
Cootow and Associates, founded by Mr Chebukati in February 2006, has represented the Independent Electoral and Boundaries (IEBC) in at least six election petitions.
"For too long and way too many times, the commission chair chair has failed to be steady and stable hand that steers ship in hard times", they said.
"However, the institution has continued to be dysfunctional with arbitrary decision making and leaking of internal documents", the resigning commissioners said in a statement. "Consequently we regret to announce our resignation from the commission with immediate effect", they said.
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"This race to chase ghosts that do not exist must stop".
They faulted Chiloba's removal saying it is a weighty matter that should not have been treated lightly.
The officers said whereas the commission is supposed to function as a single unit, Chebukati has created an "us versus them", "Commissioners versus Secretariat", and "Chair versus CEO" situation, reiterating that in their view a failure by any part of a unit of the organization is a failure of the entire commission. "All of which are against the laid down laws that govern the conduct of the commission leadership and staff", they added. "The event related to the purported vote have greatly shaken our already feeble confidence in the chair".
After the resignation of three commissioners IEBC is now left with the Chiar and only two commissioners, Prof. Abdi Guliye and Boya Molu.
One of the three officials who resigned was the vice chairman of the body.