Sheikh Salman Bin Ebrahim Al Khalifa is head of the Bahrain FA and a number of players and officials have been arrested after a campaign for political freedom began two years ago.
Salman has also been accused of vote-buying in his unsuccessful challenge in 2009 against Mohamed Bin Hammam, who has since been banned for life by FIFA.
Salman said in a statement: "I can only reiterate the fact that - in my capacity as the President of the Bahrain Football Association (BFA) - I have always been committed to manage, control and develop our game independently and autonomously without any kind of outside interference.
"I can assure anyone that the BFA is being guided according to the highest possible governance standards of integrity and transparency - fully in line with the AFC and FIFA statutes.
"As for the second part of the serious allegations which are being raised against my 2009 campaign, I can only vehemently deny this as there has never been any kind of misconduct or unethical behaviour with regards to my election programme.
"My campaign will always be based on the values of discipline and respect. I hope that - regardless of the outcome on the May 2 - all candidates will act in the spirit of fair play."
There have been claims that his campaign is again being backed by the Olympic Council of Asia which is offering grants to countries in return for their support of Salman.