The Land Rover Discovery was found intact at Thika road Mall at 1 am on Monday.
Nairobi DCI Chief Ireri Kamwende said the vehicle was intact and the search for the senior officer has been intensified.
The commission's chairman Wafula Chebukati said Musando was last seen on Friday night.
"The last communication from him is an SMS sent to one of his colleagues at around 3 am on Saturday morning," Chebukati said.
He added the content of the SMS suggested Msando was conscious and fully aware of his itinerary for the day.
"The matter has been reported to police and the commission, together with family members, is working closely with them to establish his whereabouts."
Musando was filling in for IEBC director of ICT James Muhati who was sent on a 30-day compulsory leave for not cooperating with the audit department.
Muhati was dismissed after a report by the Audit, Risk and Compliance department.
"He failed to cooperate in the provision of information requested from the department contrary to the public, finance and management regulations 2015," communications manager Andrew Limo said in a statement.
Musando was involved in the management of the KIEMS for voter registration, voter identification and results transmission.
Sources close to the commission said he helped seal loopholes that might be associated with BVR kits.
-The Star|KAMORE MAINA