Missing IEBC ICT manager Chris Musando earlier reported missing has been found dead.
He was found with one of his hands cut off.
According to police, the deputy director's body was discovered in Kikuyu and has been taken to the City Mortuary in Nairobi on Sunday.
IEBC chairperson Wafula Chebukati earlier announced Muhando's disappearance and revealed that he was last seen on Friday night.
"The last communication from him was an SMS sent to one of his colleagues at around 3 am on Saturday morning," Chebukati said.
Earlier on Monday morning, Muhando's vehicle was found at the Thika Road Mall parking lot at around 1 am.
The director is said to be among the few IEBC staff with knowledge on where the IEBC servers are.
He had earlier submitted at the Central police station a statement over death threats.