Missing IEBC ICT manager Chris Musando was found dead in Kikuyu and the body taken to City Mortuary in Nairobi on Saturday.
The IEBC acting ICT director's family members have identified the body and are at the facility.
Also at the mortuary are officials including IEBC chairman Wafula Chebukati and commissioner Roselyn Akombe.
Akombe wept and was consoled by her colleagues.
After announcing Musando's disappearance on Sunday, Chebukati said 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."
A vehicle belonging to Musando was earlier traced to the TRM parking lot. The Land Rover Discovery was found intact at about 1 am on Monday.
Musando was one of the few people with knowledge on the whereabouts of the servers at IEBC.
The manager had given Central police station officers reports of death threats.
Chebukati's security was beefed up for round-the-clock protection, three days after Musando went missing.
He has been assigned six more police officers and two chase cars.
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