Rights groups reacted with outrage, with one saying the victim had received death threats and demanding a quick inquiry into the death of the official, who had a key role in combating election fraud.
The body of Chris Msando, an information technology manager at the Independent Electoral and Boundaries Commission (IEBC), was identified at the city morgue.
"There was no doubt he was tortured and murdered," IEBC chair Wafula Chebukati told reporters.
"The only question in our mind is who (killed him) and why he was killed a few days to elections."
Msando was in charge of a system of electronic voter identification and ballot counting seen as crucial to avoid rigging. He was the number two in the commission's IT department.
All eyes are on the electronic system ahead of August 8 polls because its crash in 2013 led the opposition to accuse the election commission of rigging the election.
Msando's death follows a mysterious attack at the home of deputy president William Ruto on Saturday, northwest of Nairobi.
Police say a lone assailant killed one officer, wounded another, then held off security forces for nearly 24 hours before being killed.
Msando had helped seal loopholes that could be used to manipulate vote tallies, a source close to the IEBC told AFP.
Human Rights Watch called for his death to be urgently investigated.
"Msando's killing comes as the electoral management body was due to audit its systems, a week away from the election day," said the group's Africa researcher Otsieno Namwaya in a statement.
Chebukati announced the cancellation of that audit after Msando's killing.
'Death threats'
The Kenya section of the International Commission of Jurists (ICJ) also called for an investigation.
"Prior to his death, Mr Msando reported death threats to the central police station and the police did not provide him detailed security," it said.
"ICJ Kenya is deeply concerned with the continued unexplained insecurity incidents across the country and the extrajudicial killings."
Msando was declared missing over the weekend.
In an earlier statement, Chebukati said Msando was last seen Friday night and had sent a text message to a colleague early Saturday suggesting "that he was conscious and fully aware of his itinerary for that day".
A mortuary employee said Msando's body was brought in by police on Saturday alongside that of a woman. Both were naked and appeared to have been tortured before their bodies were dumped in a forest in Kiambu outside Nairobi.
It was unclear why it took 48 hours for his body to be identified.
Msando acted as the head of the IEBC's IT department in May after its director was suspended for 30 days for failing to comply with government auditors.
He had recently appeared on television, explaining the voting system and assuring viewers that the polls would be successful.
'Heinous murder'
Tensions have risen in Kenya ahead of the presidential election, a bad-tempered and tight race between President Uhuru Kenyatta and longtime opposition leader Raila Odinga.
Both sides have accused the other of underhand tactics; the president says Odinga is trying to divide the nation and provoke violence, while the opposition leader claims Kenyatta plans to rig the poll.
Odinga's opposition alliance condemned the "heinous murder" of Msando, saying in a statement they were "gravely concerned" about its implications.
"That no effort was made to camouflage this killing as an accident shows the determination of the killers to send a chilling message that they will stop at nothing to ensure the outcome they desire," read the statement.
While 2013's polls were largely peaceful, Kenya remains traumatised by a disputed 2007 election, which Odinga claimed was rigged.
Two months of ethnic clashes and a crackdown on protests left 1,100 dead in east Africa's richest economy, which had been seen as a bastion of stability in the region.
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