Hackers used the late Chris Msando's identity to access IEBC systems, claims NASA chief Raila Odinga who earlier dismissed poll results as fake.
Raila, who is trailing President Uhuru Kenyatta by more than one million votes, has alleged the results were manipulated.
"We have caught them. Hackers gained entry into the election database through Msando's account and directly into chairman Wafula Chebukati's account," the NASA presidential candidate told a press conference.
IEBC acting ICT director Msando, who was to test the KIEMS, was tortured and murdered. Opposition leaders blamed Jubilee but police are still investigating.
Raila said: "Hackers used Msando's details to log in to the IEBC co-server but they forgot to log out. They created errors in the server that allowed them to turn a democratic process to a function of a formula."
The Opposition leader noted a democratic process is not a show that can be manipulated at any time.
"I do this out of the obligations to Kenyans. Some people conspired and denied Kenyans the opportunity to elect their leaders."
Raila gave details of what he says followed the hacking and affected the voting process in many counties.
He said this happened in 12 hours.
He listed affected counties as Mombasa, Kilifi, Lamu, Taita Taveta, Marsabit, Isiolo, Meru, Tharaka Nithi, Embu, Kitui, Machakos and Makueni.
Others included Nyandurua, Nyeri ,Kirinyaga, Muranga, Kiambu, West Pokot, Samburu, Trans Nzoia, Uasin Gishu, Elgeyo Marakwet, Nandi and Baringo.
But Jubilee secretary Raphael Tuju earlier asked Raila to accept the people's choices and not subject them to "unnecessary drama".
"UHURU MUST GO HOME"
Raila refused to concede defeat, saying IEBC has published faulty results.
"It gives Uhuru votes that were not cast. Uhuru must go home. We do not need him as our leader and IEBC must be held accountable," he said.
"We are telling our people not to accept results, stay calm as we get deep into this."
The NASA principal further claimed no election was conducted and noted the President claimed he will win with or without votes.
"In his words, Uhuru said he did not need voters to win an election. Don't accept results that are fraudulent."
The National Super Alliance earlier rejected results of the general election saying they don't represent the will of Kenyans.
Raila said they are concerned the outcome is not in line with the law. He added it was defeating that despite IEBC agreeing to follow the law, the tallies from the constituencies were not put up.
Currently, Uhuru has 7,684,411 votes against Raila's 6,310,940 from 37,687 out of 40,883 polling stations.