Hobby ranked last in the percentage of fully certified controllers, at 56 percent, although officials for the Federal Aviation Administration say the airport has since added more certified controllers.
Hobby was followed by LaGuardia Airport in New York, with 61 percent of its controllers being fully certified, then DFW at 62 percent.
Five airports had at least 90 percent of their controllers fully certified.
Roland Herwig, an FAA spokesman, said the GAO figures were "a snapshot in time" and are now outdated.
Herwig said currently 80 percent of Hobby's 25 controllers are fully certified and that 14 of the 58 controllers at DFW are partially certified, although they are still undergoing training.
"We're recruiting, hiring and moving forward," he said. "We think we're on top of it."
Controllers are hired by the FAA, not the airports. The agency is facing a tidal wave of retirements in the next few years — 15,000 by 2017. That's because many current workers were hired soon after President Reagan fired more than 11,500 striking controllers in 1981.
The GAO, the research arm of Congress, said FAA's efforts to hire and train new workers are "generally on track, but challenges remain."
The GAO found that at some towers, experienced controllers are too busy monitoring trainees, and stress and fatigue levels are rising.
FAA officials say they are hiring new controllers.
The FAA is having trouble recruiting partly because the military, long a talent source, is offering re-enlistment bonuses up to $60,000. The FAA has expanded its applicant pool, no longer requiring that job candidates have military or FAA experience or graduate from the agency's collegiate training program, according to the GAO.
The inspector general of the federal Transportation Department also reported recently that the government is hiring so many new air traffic controllers that it can't efficiently train them.
The inspector general said the FAA has exceeded its own maximum trainee numbers at 22 percent of its 314 air control facilities.
The FAA is resisting efforts to make it publish an accurate count each year of how many fully certified controllers and how many trainees work at each of its facilities, saying the numbers change too often to be meaningful.
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