The costs charged by Spanish agency Metodo 3, appointed in September to find the missing girl, are on top of its £8,000 monthly fee - which is paid by one of the couple's wealthy supporters.
Metodo 3's expenses are the biggest single cost to the fund, which collected £1.2million in donations, but is expected to run dry within months.
It was previously thought that the agency was hired for a flat monthly fee of £50,000. But it agreed £8,000 a month, plus unlimited expenses to take on the case, which has boosted its profile.
If its "operational costs" top £50,000 the excess is met by the McCanns' wealthy backers, such as double glazing tycoon Brian Kennedy. He is to review Metodo 3's six-month contract before it expires next month.
The couple's spokesman Clarence Mitchell said the agency was "doing valuable work on the ground".
He added: '"The £50,000 is for legitimate operational costs, having people scattered around different countries. The fund contributes £50,000 a month of publicly donated money because it's money to help find her. We feel that's proper use of that money."