Mohamed Bin Hammam has claimed to FIFA's new chief investigator that Sepp Blatter appears to be untouchable.
The 63-year-old Qatari is under a provisional suspension by FIFA pending an investigation by FIFA ethics investigator Michael J Garcia.
That was launched after Bin Hammam had his life ban by FIFA on bribery charges overturned in court, due to insufficient evidence.
Bin Hammam has now written to Garcia, via his own lawyer, claiming that neither Blatter, whom he challenged for the FIFA presidency in 2011, nor other officials have been suspended despite allegations against them.
In the letter, which has been seen by the Press Association, Bin Hammam states: "Complaints have been made both against Mr Blatter and some of his colleagues which would seem to justify a full investigation.
"Whilst I am still suspended my rival in the 2011 presidential election remains in power and office.
"He is not under any investigation or suspension. This is so difficult for me to understand."
Bin Hammam claimed Blatter had used his power to crush him after he challenged him for the presidency.
He added: "In truth my previous opponent still holds all the cards. He has therefore been able to apply the full power and weight of the FIFA judicial machinery against me. I have had no relief from this onslaught for the last 16 months.
"I do appreciate that Mr Garcia has a job to do but... why should others not be suspended pending investigations in the same way that I have been?
"How can there ever have be a fair and open election in FIFA against an incumbent president? There are no rules and therefore no level playing field.
"Whilst my time to stand on a change agenda may have passed I would hope that others will follow.
"If they do so they should not be at risk of the fate that has occurred to me."
Bin Hammam, who was Asian Confederation President (AFC) and a FIFA executive committee member until his ban, said the allegations had been "a nightmare".
"I have now been kept out of football for nearly 16 months," he said in the letter. "Apart from my personal position, my family have endured the nightmare of one set of allegations after the other being made against me.
"I also have to witness the AFC, which I spent such a big part of my time and life putting into a secure financial position, beginning to crumble before my very eyes."
FIFA said they could not comment on any active cases.
Bin Hammam was accused of attempting to buy votes ahead of last year's FIFA presidential election at a specially organised meeting of Caribbean football officials in Trinidad.
The Court of Arbitration for Sport overturned the ban citing insufficient evidence but said the decision was not "affirmative finding of innocence in relation to Mr Bin Hammam".
Blatter has been previously been accused by his opponent of double standards after promising a gift of 1million US dollars to the CONCACAF federation while he was campaigning for president, and of using FIFA money to fund his campaign in terms of travel and expenses.