Bart Jansen

USA TODAY

Airlines and ticket agents are warning that hundreds of thousands of travelers might be getting overcharged on airline tickets to Alaska, Hawaii, and foreign destinations because of computer problems related to higher Transportation Security Administration fees.

As the higher fees went into effect a month ago, Sabre Travel Network, the company that provides ticket prices to travel agents and online comparison sites, told the TSA the computer problems applied to about 150,000 tickets per month in its system and 300,000 tickets per month for all reservation systems, or about 1% of all tickets.

But the airlines and Sabre haven't revealed how much money is at stake, or if anyone has indeed been overcharged.

The higher TSA fees took effect July 21, after Congress mandated them to help balance the budget.

The new fee is $5.60 for all flights, with any connection longer than four hours counting as a separate flight. The previous fee was $2.50 for any non-stop flight or $5 for any connecting flight.

Because of the new way fees are applied, which TSA announced in June, industry officials warned that computer problems could overcharge travelers on flights to Alaska, Hawaii and foreign countries when connections are longer than four hours and less than 12 hours.

Airlines for America, a trade group, repeatedly asked for 90 days — or until mid-September — to adopt computer changes for those flights. The airlines and Travel Technology Association told the TSA that all changes could be remedied by Sept. 30.

Anytime the government asks for complex technical changes, said Philip Minardi, a spokesman for the tech group, "it's important that they consider the significant programming, testing and quality-control measures needed to accomplish the task."

But the TSA rejected the request in a July call with industry lawyers, saying the industry expected to handle 99% of the itineraries correctly and could offer travelers refunds if they are overcharged. The TSA said delaying the higher fees would hurt the federal budget.

Sabre said 99% of tickets should be accurate, but the remainder could be overcharged. Sabre warned that rushing and cutting corners to fix problems for the inaccurate tickets could further delay the program.

The TSA expects to collect $3.6 billion per year in fees to start, so 1% would be $36 million, but that doesn't specify how much the mistakes would total.

Asked for comment, Alaska Airlines deferred to the trade group, and Hawaiian Airlines didn't respond.

An A4A spokeswoman referred to the group's Friday statement to the TSA from general counsel David Berg, who said the computer-programming requirements "were extremely complex and required extensive changes to existing systems."

The deadline was Tuesday for comments about the higher fees. The TSA collected nearly 600 comments, with many opposed to the higher charges.

And the airline group, A4A, is challenging the fee hike in the U.S. Circuit Court of Appeals for the District of Columbia.