Stakeholders, led by former Federation president Sam Nyamweya and former Council for East and Central Africa Football Associations (Cecafa) secretary-general Nicholas Musonye among others, had filed a petition to stop the elections stating there were no guarantees the exercise would be credible.
Sports Registrar Rose Wasike followed up with a letter to FKF secretary-general Barry Otieno, advising the Federation to put their house in order before proceeding with the exercise.
The Elections are set for Saturday, October 17
The Registrar had argued the register used was faulty and was not verified.
However, Sports Disputes Tribunal (SDT) chairman John Ohaga dismissed the case, stating the reasons presented were not weighty.
He argued that one of the petitioners, Omondi Aduda, had even presented his papers to the Electoral Board and is among those who will be on the ballot box for the elections set for this weekend.