FIFA has hired the ex-FBI chief's investigative agency, Freeh Group International Europe, to work on the probe and Caribbean federations have been asked to attend interviews in Miami on Tuesday and Wednesday, a Caribbean football source told Reuters on Monday.
But the choice of a high-profile American to head the probe has led at least one Caribbean football federation to ask Blatter to intervene.
"The investigation is tainted and biased and clearly has a U.S. driven agenda," a federation official wrote in a letter to FIFA seen by Reuters.
The official said there were "two America complainants, an American investigator, an investigation and an interrogation being conducted on American soil while FIFA remains a Swiss registered entity and none of the persons under investigation being U.S. citizens"
The letter asked FIFA President Sepp Blatter to replace Freeh with a "truly independent investigator and secure a neutral venue for the interview of any Caribbean Football Union member other than the United States of America."
Three members of the Caribbean Football Union (CFU) - president Jack Warner and staff members Debbie Minguell and Jason Sylvester - were provisionally suspended by FIFA's Ethics Committee pending a full inquiry into the events surrounding a meeting in the Caribbean with Asian football chief Mohamed Bin Hammam.
The report to FIFA's Ethics Committee was initiated by American Chuck Blazer, general secretary of CONCACAF, the regional body for football in North and Central America and the Caribbean.
Barbadian Lisle Austin, who replaced Warner as interim president of CONCACAF, was suspended by that body's executive committee on Friday and Honduran Alfredo Hawit was appointed to replace him.
Jamaican Horace Burrell remains a member of the executive but his name has not featured in statements, such as the one suspending Austin, which have been issued in the name of the 'majority of the executive'.
