The $10million payment sent from FIFA to Jack Warner never appeared in the annual accounts of the Caribbean Football Union, while FIFA failed to track the money to ensure it had been invested correctly.
The money, which according to a US justice department indictment was a bribe for Warner and his deputy Chuck Blazer to vote for South Africa to host the 2010 World Cup, was sent in 2008 and officially destined for the CFU as a legacy programme to support football in the Caribbean.
Instead, the money was removed from the CFU bank account in New York and used by Warner in a number of ways, including paying Blazer $750,000.
The bribery scandal has caused a crisis in the world governing body and last week Sepp Blatter announced he is to step down as FIFA president.
The CFU's financial statement for 2008 makes no mention of the $10million payment going through its bank account, stating that its only revenue was $1million from tournament sponsorship and $15,000 in membership dues.
The CFU audit was carried out by Kenny Rampersad, who was also the personal accountant of Warner and Blazer.
The $10million did not show up in the 2008 financial statements of the CONCACAF federation either - Warner was president of both that organisation and the CFU.
FIFA insists that "member associations and confederations have to provide FIFA with an audited financial statement every year"... to ensure that "all financial assistance payments are invested correctly".
However, the organisation said it had not had the right to audit the CFU.
A FIFA spokesman said: "The Caribbean Football Union is not a member association of FIFA, so FIFA has no right to audit it and has not done so."
The $10million payment was paid by FIFA to Warner at the request of South Africa, but is not itemised in FIFA's 2008 accounts.
FIFA's auditors KPMG did not flag up the payment in its annual report and would not comment on the case, saying in a statement: "As FIFA's statutory auditor, we are bound by professional confidentiality and have to refrain from any comment regarding our client."
FIFA has said it merely "facilitated the reallocation" of funds destined for the World Cup to Warner at the request of South Africa. The South African government has insisted the money was not paid as a bribe.
Blazer has however pleaded guilty to taking the money as a bribe to vote for South Africa following a deal agreed in 2004 involving "high-ranking officials of FIFA, the South African government, and the South African bid committee", according to the US indictment.
Rampersad's involvement as an auditor was criticised by a 2013 report by CONCACAF's integrity committee instigated following Warner's resignation in 2011.
That report stated: "Warner and Blazer had arranged for the audits to be conducted by Kenny Rampersad, an accountant who clearly lacked the independence to conduct a proper audit and did not engage in activities one would associate with an audit.
"A review of the evidence showed that the auditor used by CONCACAF - Kenny Rampersad & Co - was not independent and in fact possessed clear conflicts of interest."
According to the Trinidad Express, Rampersad is also the company accountant for the Trinidad-based JTA supermarket group, and it was he who carried out foreign currency purchases for the company from the $10million from Warner's account.