The resignation comes after Chebukati suspended CEO Ezra Chiloba over irregularities in the procurement process.
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.
One of those who resigned is the vice chairman of the Independent Electoral and Boundaries Commission.
Three Independent Electoral and Boundaries Commission (IEBC) Commissioners have announced their resignation from the agency citing lack of confidence in Chairperson Wafula Chebukati. There are no longer good or bad commissioners at IEBC.
In his affidavit, Chiloba had told the court that the decision to have him go on compulsory leave was prejudicial since he was not accorded an opportunity to defend himself.
The fallout now leaves it with chair Wafula Chebukati, Prof.
"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. The latest resignation of three commissioners may create another heated political exchange.
With the three commissioners resigning and another fleeing the country previous year, the two remaining commissioners and Chebukati will be unable to make decisions. The commission was frequently at the centre of controversy during Kenya's extended election season previous year, in which around 100 people were killed. "All of which are against the laid down laws that govern the conduct of the commission leadership and staff", they added.
FILE - Kenya's Supreme Court judges attend a hearing regarding petitions challenging the result of the presidential election re-run at Kenya's Supreme Court in Nairobi, Nov. 14, 2017.
Opposition leader Raila Odinga boycotted the repeat election, which saw President Uhuru Kenyatta being elected for a second term.
Kenyatta won reelection after the main opponent dropped out of the race, saying electoral officials failed to make necessary reforms.