FIFA is expected to show a loss of at least $100 million when it publish the 2015 financial report next month.
Acting FIFA secretary general Markus Kattner says staff confidence has been hit by a looming $550m financial deficit, telling the FIFA election congress that there is "general uncertainty that is affecting morale of the FIFA team."
The acting secretary general added that the sport's governing body "are currently behind our goals" to reach a budget target of $5b revenue from the 2018 World Cup in Russia.