The development comes after Chebukati sent CEO Ezra Chiloba on compulsory leave even as the Commissioners claimed they were not consulted.
The commissioners said they chose to step down after Ezra Chiloba, chief executive of the Independent Electoral and Boundaries Commission (IEBC), was suspended pending an audit on procurement matters.
In a statement, the three commissioners accused the chairman, Wafula Chebukati, of turning the commission into a space for "scrambling and chasing individual glory and credit".
"We must banish external players from the commission boardroom and reclaim the commission's independence", she said.
Chebukati alongside Commissioners Abdi Guliye and Boya Molu supported the motion which was precipitated by an internal audit that unearthed non-adherence to procurement laws and plenary guidelines in the award and execution of five tenders in the period leading to last year's elections.
"The Commission Chair has failed to be the steady and stable hand that steers the ship in hard times and gives directions when needed", they noted in a statement.
Three Kenyan election officials resigned yesterday, increasing chaos at the electoral commission after last year's botched presidential vote that had to be rerun and was then boycotted by the opposition.
The legislator now wants IEBC Chairperson Wafula Chebukati to resign as well to pave way for lasting reforms in the commission. "It has become increasingly hard to appear on television to defend positions I disagree with in the name of collective responsibility", said Dr Akombe in her statement announcing her resignation.
Magaya proposed that in future, political parties be tasked with nominating IEBC commissioners. I am yet to receive formal communication on this matter. "We think that this is a culmination of leadership failure in the commission and its important that Chebukati takes action to resign from his office now, with the remaining two commissioners".
"Without a doubt a doubt it undermines the legitimacy of the Jubilee administration and confirms that its election was an electoral fraud", he added.
The commissioners handed Chebukati a sweeping condemnation for incompetence saying he has made IEBC a dysfunctional body. "The organization is cursed", Orengo said.