Airlines frequently charge extra for things like baggage and cancellations. A stipulation requiring airlines to curb their extra fees was stripped from a funding bill for the Federal Aviation Administration. (Patrick Semansky/AP)

Congress protected the $4.6 billion in fees that U.S. airlines charge for baggage, seat assignment and flight changes as part of a late-night action to continue funding for the Federal Aviation Administration.

The fees — described by one aviation expert as “the biggest complaint of the flying public” — would have come under scrutiny by the U.S. Department of Transportation if a House-Senate committee had agreed to the language in the bill.

But the legislation announced at 2:52 a.m. Saturday removed a provision that would have allowed the DOT to decide whether airline fees were “unreasonable” or out of line with the cost of providing the service in question.

“Airline travelers are being gouged by exorbitant fees, but the airlines will stop at nothing to protect this billion-dollar profit center,” said Sen. Edward J. Markey (D-Mass.), an author of the provision.

Markey said that “through an opaque negotiating process, the airlines have managed to kill this important consumer protection provision.”

Airline fees that are above and beyond the cost of a ticket amounted to almost $2.4 billion in the first half of this year, and the federal Bureau of Transportation Statistics said they totaled $4.6 billion last year.

Airlines already have contributed $2.4 million to incumbents in Congress for the election cycle that ends with the Nov. 6 election, and in the past 10 years, incumbents have received $12.4 million from the industry, according to the Center for Responsive Politics.

Word of a final deal came eight days before Congress faced a deadline for approval or extension of the bill. The FAA has been hamstrung for more than a year — with three funding extensions — by congressional disagreement of how the agency should be funded.

The five-year reauthorization bill provides several passenger protections and addresses some high-profile airline issues. It instructs the FAA to set minimum passenger entitlements for leg room and width of seats. It prohibits involuntary bumping of passengers who have boarded a plane, a nod to the now infamous incident in which United Airlines passenger David Dao was dragged from an aircraft last year when he declined to give up his seat.

The bill also requires the DOT to establish an aviation consumer advocate to help consumers resolve air travel complaints. It regulates operation of drones, sets requirements for flight attendant rest periods and requires better communication between airlines and passengers over canceled flights.

“After several weeks of negotiations, I am pleased that we can announce a bicameral, bipartisan multiyear reauthorization of the FAA,” House Transportation Committee Chairman Bill Shuster (R-Pa.) said in a statement.

The committee’s ranking member, Peter A. DeFazio (D-Ore.) in a statement said, “While this legislation isn’t perfect, it is the product of a strong bipartisan effort that will improve and advance the U.S. aviation system for years to come.”

Airlines began imposing fees in 2007, when the Bureau of Transportation Statistics said 22 of them collected $464 million for various specified items. If the balance of the current year mirrors that of its first two quarters, the airlines will collect fees of more than $4.7 billion by year’s end.

Brent D. Bowen, a dean at the Embry-Riddle Aeronautical University in Arizona who for 28 years has put out the Airline Quality Rating, said last week that “the biggest complaint of the flying public right now is always about fees.”

“People don’t realize what their getting into when they go into the purchase process,” he said.

Shopping for the best bargain on an airline ticket, passengers often discover that fees for baggage, better seats and changes in flights mount suddenly.

Sean Kennedy, a vice president at Airlines for America, a lobbying group for several key players in the industry, said airlines are doing a better job of cautioning would-be passengers about fees they might incur.

“What you’ll see is that the airline websites are getting in­cred­ibly better at communication,” Kennedy said. “ ‘Are you sure you want to purchase this? Do you recognize that this is what you cannot get [at this ticket price]? Are you sure you recognize that this ticket is not refundable?’ ”

The airlines contend that the move toward a base ticket price, with other things added on, including for items like overhead bins for carry-on luggage, are being driven by ultralow-cost carriers.

“There’s a growing number of consumers who want the lowest fare possible,” Kennedy said. “And if they want to put add-ons to make their flight a better experience for them, that’s the way they want to do it. The Spirit [Airlines] model: You get a cheap seat, and you don’t get much else.”