The officials were part of the Independent Electoral and Boundaries Commission.
Magaya also alleged IEBC Vice Chair Consolata Maina, commissioners Paul Kurgat and Margaret Mwachanya were working for Deputy President William Ruto. "Consequently, we regret to announce our resignation from the commission with immediate effect".
The development comes after Chebukati sent CEO Ezra Chiloba on compulsory leave even as the Commissioners claimed they were not consulted.
Mwachanya blames politicians for the commission's woes. "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".
"Under the current commission leadership, we have had many instances where statements have been issued purporting to give a position of the commission, yet those statements are a misrepresentation of facts", they said, adding that the events in the last 10 days are a clear manifestation of the dysfunction. He said he knew of their resignation through the media like every other Kenyan.
"The removal of a CEO is a weighty matter, and is one that should not have been introduced as a by-the-way", the commissioners said in reference to the argument that Mr Chebukati had ambushed the other commissioners with the agenda.
The commissioners' resignation leaves in office three other commissioners after Roselyn Akombe resigned in October past year saying she feared for her safety and that the IEBC as then constituted could not hold credible repeat elections.
The commission is now crippled as it lacks the quorum of five commissioners to transact business as required by law.
"The challenges of the 2017 elections call for the commission to self-reflect and to institutionalize best practices".
While confirming Chebukati's return to the country from an election conference in Nigeria, IEBC Communications Manager Andrew Limo had told Capital FM News that there was no plenary meeting scheduled for the day.
Three Kenyan election officials resigned on Monday, increasing chaos at the electoral Commission following last year's botched presidential vote that had to be rerun and was then boycotted by the opposition.
Magaya proposed that in future, political parties be tasked with nominating IEBC commissioners.