The accounting records of the Confederation of African Football (CAF) have been described as "unreliable and not trustworthy" after an independent audit, it has been reported.
A review of the troubled organisation was made by PricewaterhouseCoopers (PWC) with their findings seen by Reuters.
According to the news agency, a "series of concerns" have been listed over 55 pages.
The findings come after FIFA announced earlier this month that its "six-month mission" to reform African football had been "successfully completed".
In a statement the world governing body acknowledged the PWC report alongside a series of recommendations, but the document has not been made public.
"The accounting records of CAF are unreliable and not trustworthy," the report reads, according to Reuters.
"Based upon the procedures performed and documents reviewed, several red flags, potential elements of mismanagement and possible abuse of power were found in key areas of finance and operations of CAF.
"Given the serious nature of certain findings and red flags identified from the preliminary due-diligence, we cannot rule out the possibility of potential irregularities."
The report claims that many transactions were made with cash, which would not leave an audit trail.
BBC Sport has reported that a 2017 deal with Tactical Steel is of particular interest, as it is allegedly worth four times as much as an arrangement cancelled with sportswear giant Puma.
An associate of CAF President Ahmad, who has denied wrongdoing, has alleged links to Tactical Steel.
Payments between CAF and French media company Lagardere, and the distribution of money from the FIFA development fund, have also been highlighted.
The possible mismanagement of the CAF Centre of Excellence in Cameroon is another issue, BBC Sport said.
FIFA effectively took over control of the CAF in July following a series of allegations levelled at Ahmad, who is from Madagascar.
Secretary general Fatma Samoura was placed in charge of a group overseeing day-to-day operations by FIFA President Gianni Infantino.
Ahmad, who goes by one name, was arrested over corruption charges in Paris in June and has also been accused of sexual harassment.
He has been subject to investigation by FIFA's Ethics Committee but has not faced suspension.
When announcing that FIFA's work had been completed earlier this month following a meeting in Morocco's capital Rabat, Samoura said "three pillars" had been focused on.
These were "good governance, financial management and internal procedures", "efficient and professional organisation of competitions" and "growth and development of African football".
A 100-point action plan on good governance would be implemented, FIFA said, while a $1 billion (£775 million/€910 million) infrastructure fund to invest in all 54 African member associations was called for.
Other recommendations included the creation of a group of professional referees and seeking new initiatives in international, club, women's and youth football.
In line with a strategy presented by Infantino, a Pan-African League could be created.
"As agreed at the beginning of the mission, a forensic audit report produced by PricewaterhouseCoopers was presented," FIFA said.
"FIFA is satisfied that the joint effort made with CAF was done and delivered within the initial proposed time-frame and reiterates FIFA's commitment to be at the disposal of African football to assist in the process of raising its level to the top of the world."