Chris Msando was head of information technology for Kenya's Integrated Electoral Management System. His department was responsible for voter identification and result transmission technology for the August 8 elections.
Msando had last been heard from early Saturday -- when he sent a text message to a colleague.
"We learned in shock, the killing and murder of our employee, Chris Msando. There's no doubt that he was tortured and murdered," Independent Electoral and Boundaries Commission Chairman Wafula Chebukati said Monday. Msando's death has raised fresh fears over Kenya's ability to deliver credible elections.
"The only issue is who killed him and why ... I demand from the government that they provide security for all employees of IEBC, for us to give Kenyans a free and fair election," Chebukati said.
Election observers from the nongovernmental watchdog Carter Center had said in a pre-election statement that the smooth functioning of the voter identification system was key to "preventing malpractice on election day."
Efforts by CNN to get a comment on the case from police were not immediately successful.
Kenyatta opposed by longtime rival Odinga
Voters in the east African nation are due to go to the polls next week with incumbent President Uhuru Kenyatta looking to secure a second five-year term.
If no winner is declared, the election will go to a runoff, which would be a first in Kenya's history.
Otsieno Namwaya, an Africa researcher at Human Rights Watch, issued a statement urging Kenyan authorities to "urgently" investigate the circumstances surrounding Msando's death.
"Msando's killing comes as the electoral management body was due to audit its systems, a week away from the election day," Namwaya said.
While Amnesty International's Kenya researcher Abdullahi Halakhe said the death so close to election day should be a red flag to Kenyan authorities.
"Next week's vote will be extremely close and there is a very real danger that the situation will erupt if the authorities do not ensure that the Kenyan people are able to cast their votes free from intimidation, threats and violence," Halakhe said.
Msando had been due to oversee public testing of the election management system Monday.
In 2013 a breakdown in voter identification technology was a primary reason that Odinga contested the results,