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The Paul Ryan-Patty Murray budget deal, reached Tuesday night, could help avert another government shutdown in Washington, but will airline passengers around the country have to pay for it?

By eliminating $65 billion in across-the-board domestic and defense cuts, the Bipartisan Budget Act of 2013 puts an end to the sequester, but to make up for a portion of those savings, the budget deal includes an increase that more than doubles TSA security fees for airline travelers.

Prior to the budget deal, the president and CEO of the trade organization Airlines for America, Nicholas E. Calio, said in a statement, "Doubling the TSA passenger security tax would cost passengers more than $730 million annually, placing a huge additional tax on the traveling public, with no direct benefit to those who pay it."

Today, in a statement to ABC News, Katie Connell, a spokesperson for Airlines for America, reiterated Calio's concerns. "We recognize the difficult decisions that led to a bipartisan effort to restore certainty to the budget process," McConnell said. "As we have said consistently, airlines and our customers are already overtaxed, and we are disappointed that fees on air travel were increased, and believe those higher taxes will impact demand, jobs and our economy."

The increase in fees comes from an increase to the aviation passenger security fee, also known as the "9-11 fee."

Prior to Sept. 11, 2011, airlines were responsible for paying for and carrying out their own passenger and baggage security screening, but with the creation of the Transportation Security Administration, passenger and baggage screening became centralized and government-operated.

In order to help pay for the new agency and heightened airport security procedures, Congress enacted the Aviation and Transportation Security Act. The TSA currently receives approximately $2 billion a year from this current law from air carrier and aviation passenger security fees, which cover 30% of the agency's aviation security costs.

Initially, the aviation passenger security fee was established and currently remains at a charge of $2.50 per nonstop flight, and $5.00 for a flight that requires a connection.

The newly proposed budget act changes the fee structure, and more than doubles the fee for a one-way flight to $5.60, making a round-trip flight fee $11.20. The new fee does not include an increase for connecting flights.

According to the Bipartisan Budget Act of 2013, the higher fee will enable the TSA to offset approximately 43 percent of its security costs and eliminate the aviation infrastructure security fee charged to air carriers.

Calio also notes that increasing the TSA security fee "won't improve airport security, but instead will negatively impact customers by driving up the cost of air travel. Congress should instead focus on improving the efficiency of TSA, which collected $2.3 billion in security taxes from airlines and their customers last year, more than double the amount collected in 2002."

The budget deal requires that the heightened security fee be effectively changed by July 1, 2014.

House Budget Chairman Paul Ryan stands behind the proposed bipartisan budget deal. "I'm proud of this agreement," said Ryan said in a statement announcing the budget agreement. "It reduces the deficit - without raising taxes. And it cuts spending in a smarter way. It's a firm step in the right direction, and I ask all my colleagues in the House to support it."