Engineer Mruttu garnered 15,911 votes while his rival,Wundanyi Member of Parliament Thomas Mwadeghu, secured 18,421.
Following the loss, the Governor released a statement terming the nomination process unfair.
He noted that he had written to the ODM National Elections Board outlining various conflicts of interest involving the County Elections Board (CEB).
The incumbent governor accused the CEB Secretary of organising a meeting for the board members at the home of one of the aspirants who is also the Secretary's known acquaintance.
Mruttu also agonised over the method used to select the polling stations, claiming that it was suspicious that polling stations with high voter population were left out.
The governor claimed that the list of Presiding Officers released 24 hours to the nomination day comprised of well-known campaigners of the aforementioned candidate.
He added that the same officials were not available to conduct the process for most of the day in some of the polling stations.
"Voters in Taveta feel that there was a deliberate attempt to sideline them and deny them their fundamental right of participating in electing leaders," the statement read in part.
The Governor concluded his statement by noting that he had received verbal confirmation that some of the constituencies would conduct the polls on Thursday, however, results were announced on Wednesday afternoon.
"I have since checked with the chairman of the county elections committee who appears completely lost and unaware of any such plans," he stated.