The FAA's poor track record of containing costs is well-documented. For example, in 2003, the Government Accountability Office, Congress' investigative arm, reported the agency's ongoing efforts to modernize air traffic control and found the price tag had reached $35 billion — nearly three times the original estimate of $12 billion when the project began in 1981. Much of that money also came directly from airline passengers in the form of ticket taxes.

"Then was then, now is now," said FAA spokeswoman Laura Brown, adding that Blakey has drastically tightened FAA financial management since becoming agency administrator in 2002. "The way we manage programs is dramatically different."

Former Pennsylvania congressman James Coyne, now president of the National Air Transportation Association, said that doesn't negate the fact that the federal government has squandered aviation money over the past two decades.

"Certainly billions of dollars were wasted because of mismanagement," said Coyne, whose group represents charter, tour and commuter aviation operators and opposes eliminating passenger taxes. "Now, there must be some accountability."