By Claire Zillman
March 12, 2014

FORTUNE — Zachary Wilkinson was just a few months into his freshman year at Embry-Riddle Aeronautical University when the path he’d set out for himself — earning a degree in aeronautical science and landing a job as a commercial pilot — was upended.

In February 2012, the Federal Aviation Administration proposed a rule that would require first officers — commercial airlines’ entry-level pilots — to hold an Airline Transport Pilot certificate, which requires 1,500 hours of flight time. Graduates of programs that have been approved by the FAA, including Embry-Riddle, could earn an ATP with 1,000 flying hours. The rule was proposed in the wake of the February 2009 crash of a Colgan Air regional plane caused partly by pilot fatigue, and it became law in August 2013.

Wilkinson, 21, will leave Embry-Riddle with a bachelor’s degree and about 250-300 hours of flying time. He enrolled at the university thinking that would be enough to land him in the co-pilot seat at a regional airline. But when Wilkinson graduates in the spring of 2015, those 300 hours in the air will leave him 700 hours short of an entry-level airline job.

“It was discouraging,” Wilkinson tells Fortune. “It will require me to spend more time building up hours as a flight trainer.” Wilkinson now plans to apply for a flight instructor position at Embry-Riddle after graduation. Working in that role for a year or so will put him over the 1,000-hour threshold.

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The gap between the flight time required to be a commercial pilot and the hours that students like Wilkinson log in college is another factor in the impending pilot shortage. Late last month, the U.S. Government Accountability Office released a report that said regional airlines are having trouble finding enough qualified individuals to pilot their planes.

One commonly cited culprit in the shortage is pilots’ measly first-year pay. The GAO report pegged it at $24 per hour based on data collected for 14 regional airlines, but the Air Line Pilots Association estimates that the average starting salary is even lower than that — $22,500 per year, which for a 40-hour work week equals an hourly rate of $10.75.

The pilot lifestyle — especially at the regional level, where pilots jet from one small market airport to another — also plays a role. Kent Lovelace, professor and chair of the aviation department at University of North Dakota, said that when his school surveys students about why they don’t want to be an airline pilot, they most frequently cite the lifestyle. Pay is the second-most frequently mentioned deterrent, he says.

But the new flight hours requirement means that the thousands of college graduates in flight programs — there were 10,600 in 2008, the last time the University Aviation Association took count — can’t immediately fill the roughly 1,900 to 4,500 new pilot positions that the GAO predicts will open up annually for the next 10 years. Instead, they have to spend at least another year after graduation logging hours to get the same job that a previous generation of pilots could secure fresh out of school.

“The shortage is with these new pilots and the changed criteria,” says Tim Brady, dean of Embry-Riddle’s college of aviation. It’s getting so critical, he says, “regionals are starting to park their planes.”

The best way to rack up hours is to become a flight instructor, but those positions are limited. For instance, Embry-Riddle employs 150 flight instructors, and it graduates between 300 and 400 students from its flight program every year, says Brady. Graduates who can’t land a flight instructor job have to resort to gigs like flying planes that tow banners or crop dust to surpass the 1,000-hour mark.

It’s too early to tell how the new flight time requirement will affect student enrollment in aviation programs. Universities like Embry-Riddle and UND, which have had their curriculum approved by the FAA and whose students qualify for the 1,000-hour exemption, have a recruiting advantage over colleges that haven’t met those requirements. But even before the new regulation went into effect, Lovelace says UND’s piloting program was facing increased competition from careers in operating unmanned aircraft systems, or drones, which UND began to offer as a course of study in 2009.

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“If you turn the clock back 15 years, 75-80% of our student population was interested in professional flight. Now that’s about 55%,” says Lovelace, who notes that completing the flight program at UND costs in-state residents about $120,000. Half of the cost is for flight time.

Universities and airlines — and passengers, for that matter — will have to hope that students with an interest in commercial flying will look past the large initial training investment and focus on the profession’s long-term benefits. Median pay for airline and commercial pilots in 2012 was $98,410, according to the Bureau of Labor Statistics.

Or they can bank on the notion that there are many more Zachary Wilkinsons out there, itching to get into a cockpit. “If I was doing this just for the paycheck, I wouldn’t be here. I’m doing it for the prospect of providing a great service to people and for the travel and adventure of it,” he says. “I’m willing to spend the first few years climbing the ladder.”

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