Earlier, Sofapaka president Elly Kalewkwa claimed Muthomi was acting as Avire's agent and he was secretly influencing his transfer to an unnamed club in Egypt.
Muthomi also welcomed the expected investigations promised by FKF president Nick Mwendwa on the matter.
"I emphatically deny the allegations made against me that I have tried to coerce the player (John) Avire to terminate his contract with Sofapaka FC," Muthomi said in a press statement seen by Goal.
"Given the gravity of the unfounded claims and for the purpose of openness, I welcome the pronouncement of FKF president that the matter will be investigated thoroughly by the relevant organs of FKF.
"I expect the investigations will go to the core of the matter and I look forward to being vindicated."
While Muthoni is unmoved by whatever criticism comes his way as an official of the FKF, he is adamant he will clear his name over the allegations emanating from the Avire transfer saga.
"While by virtue of my position in the federation and the nature of the job of the general secretary, constant criticism during the discharge of my duties is expected and rarely elicits a response, I find it necessary to defend myself on this thoughtless accusations," Muthomi added.
Although FKF promised to look into the matter, it is yet to provide an expected timeline of the investigation.