"I am concerned that there is a disproportionate impact on customers, who may be being charged unfairly high fees," he said in the letter.
"Further, I query whether customers are being misled in that context.
"I would be grateful if you could consider using the powers available to you to require Qantas and other airlines to substantiate their claims that the fuel surcharge is needed to recover their additional fuel charges."
Flight Centre managing director Graham Turner lashed out at fuel surcharges on Thursday, saying recent reductions had seen fuel prices fall to their lowest levels in more than year and should prompt airlines to lower the levies and change their complicated fuel surcharge structure.
The travel company found that fuel prices had tripled since modest surcharges were first introduced in 2004 but that the levy had typically been raised by many times that amount.
It said Qantas's current $760 surcharge on a return flight to London was more than 12 times its initial surcharge of $60 and the levy had not dropped since March, 2009.
Fuel surcharges also varied from airline to airline with Flight Centre's analysis showing British Airways charges $763, Malaysia Airlines $590, Virgin Atlantic $580, Singapore Airlines $571 and Cathay Pacific $532 on flights between Australia and London. It said Air New Zealand did not have a fuel surcharge and Qantas partner Emirates had "a relatively small fee".
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