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The South African Football Association (Safa) made a loss of R54.4 million for the year to June 2012.
According to a KPMG-audited financial statement, Safa spent R27.5 million last year, leaving it with R2.9 million in the bank, while salaries came to R17.1 million.
Safa received R113 million from the "Fifa World Cup Legacy Fund" for the development of football.
Safa's former CEO Robin Petersen said only a small part of that amount was paid in cash as it included assets such as buses, X-ray equipment and fencing.
He admitted Safa faced "serious challenges" in terms of its cashflow after main sponsors Absa and Castle Lager had cut their sponsorships.
