Chebukati stated that he was yet to receive the formal communication confirming the resignation of commissioners Connie Nkatha Maina, Margaret Mwachanya, and Paul Kugat.
Experts said the effect of the latest move will destabilize the commission at a time it is preparing to conduct electoral boundaries review for the 2022 election, whereas Chiloba's absence will make it hard or impossible for the secretariat to operate because the CEO by law makes the day-to-day decisions which no other commissioner can.
Kenya's electoral body was on Monday thrown into turmoil after three commissioners resigned, citing loss of confidence in the chairman.
"Henceforth, political parties should nominate IEBC Commissioners".
The latest development dividing the commissioners was the suspension of the head of the commission's administrative wing, Ezra Chiloba over financial mismanagement.
The commissioners said they hope that their resignation will accord an opportunity to reflect on the future of the electoral body.
Senator Kipchumba Murkomen of the ruling Jubilee Party is now calling for commission head Wafula Chebukati to step down and for the IEBC to be disbanded.
"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 commissioners a year ago refused to step down amid opposition calls on them to resign, followed by protests to force their resignation, leading to scores of deaths. "And pursuing of personal interests", the commissioners said in a statement.
Last year's election re-run raised fears of a return to political violence in Kenya where more than 1 200 people were killed after a disputed poll in 2007, although President Uhuru Kenyatta and opposition leader Raila Odinga appeared to put their fierce rivalry behind them last month.
Last September, Kenya's Supreme Court annulled the August 8 presidential reelection of Uhuru Kenyatta and ordered a do-over.
Kenyatta won reelection after the main opponent dropped out of the race, saying electoral officials failed to make necessary reforms.