Airline miscues — such as the computer glitches that grounded hundreds of thousands of passengers this summer — are now the biggest cause of flight delays in the U.S.

Late arrivals triggered by mechanical breakdowns, a lack of flight crews and other factors attributed to the airlines were the largest category of delay last year for just the second time, and by the widest margin, since the government began collecting such data in 2003.

It exceeded what had been traditionally the biggest causes: weather and hiccups in the Federal Aviation Administration’s air-traffic system, according according to data provided by the airlines to the Department of Transportation’s Bureau of Transportation Statistics.

“They don’t have any give in the system anymore,” said Charlie Leocha, president of Travelers United, which advocates on behalf of passengers. “I think a lot of it has to do with this drive to profitability.”

The 323,454 flights delayed last year due to the airlines exceeded the number attributed to the FAA by 6,770, the biggest margin ever. Almost six out of 100 flights were held up by factors attributed to the airlines. That doesn’t include the ripple of delays that a late flight inflicts on subsequent ones.

And the difference is even more substantial when measured by the aggregate amount of time flights are tardy. Airline-caused delays totaled 20.2 million minutes last year — 2.7 million more than all other categories combined.

Airlines for America, the Washington trade group representing most of the large carriers, said the government numbers don’t tell the whole story. Airlines helped the system achieve an on-time rate of about 80 percent by reducing the number of flights, which eased congestion at the busiest airports, Sharon Pinkerton, the group’s vice president for legislative and regulatory policy, said in an interview.

“I do think that is a major part of the context that we need to be talking more about,” Pinkerton said.

A delay is defined as any flight that reaches the gate at least 15 minutes later than its scheduled arrival time. Delays attributed to the airlines include such factors as maintenance, pilots who didn’t arrive on time, aircraft cleaning or baggage loading.

Or, as some unlucky passengers recently learned, computer glitches. A power loss at Delta’s computer center on Aug. 8 prompted more than 2,000 canceled flights worldwide. A computer failure at Southwest Airlines Co. on July 20 is expected to cost “tens of millions” of dollars after more than 2,300 flights were canceled, the company said.

Delays in recent years are far less severe than the period from 2006 through 2008, when there were more flights and carriers fought fiercely for market share at overburdened airports such as those around New York and Chicago. Since then, airlines deserve credit for cutting flights and working collaboratively with the FAA, according to the agency and academics who have studied the data.

That has reduced the delays attributed to the FAA system.

But the swelling share of airline-caused flight delays marks a sea change from the days starting in 2003 when passenger outrage prompted regulators to require carriers to report the reasons flights were delayed. For much of the 2000s, late flights attributed to the aviation system far exceeded those by the airlines.

That trend has gradually reversed itself, according to the U.S. data.

Last year the carriers caused 20.2 million minutes of delays, according to their own reports to the government. The category known as “National Aviation System” — mainly weather, congested airports and problems with the air-traffic system — led to 14.3 million minutes of delay.

Other categories are reserved for severe weather events, such as hurricanes or snowstorms that shut down airports, and security delays. Even when combined with the national aviation delays, the total, 17.5 million minutes, is still less than the airline-caused ones.

Planes were held up for another 25 million minutes last year for undetermined reasons because the previous flight arrived late, something that reverberates through the system, according to the data. That type of delay is not attributed to the carriers in the data.

The existence of these unexplained delays “muddies the picture quite a bit” and makes it difficult to conclude what is most responsible for slowing flights, Pinkerton of Airlines for America, said. Airlines have also added to the scheduled times it takes to fly between many cities, which artificially reduces delays, she said.

“Part of the reason that number is so good is we have adjusted our scheduling to basically cover for” the air-traffic system’s inefficiencies, she said.

At least one airline doesn’t agree with the trade group’s position. Delta Air Lines Inc., which split from Airlines for America last year and has the best on-time record of any major carrier, believes the nation’s air-traffic system is “far from broken,” Chief Executive Officer Ed Bastian wrote in an opinion piece posted on the airline’s website in April.

“The fact is the current air traffic-control system, run by the Federal Aviation Administration, is the same for every airline operating within it,” Bastian wrote. “What sets Delta apart is that we have invested in our people, our operation and our technology to enable us to outperform our competitors within the system where we all operate.”

Delta last year had fewer flights delayed due to its own operations, 4.4 percent, than any of its large U.S. competitors, according to the data. All airlines averaged 5.6 percent for such delays last year.

United Continental Holdings Inc. and American Airlines Group Inc. each referred to Airlines for America for comment on the delay numbers. JetBlue Airways Corp. believes airline efforts to smooth traffic flows “are masking underlying inefficiencies of the air-traffic control system,” spokesman Doug McGraw said.

Partially as a result of these issues, members of Congress and most of the large airlines have called for placing the government’s air-traffic system into a nonprofit corporation, arguing that it uses outdated technology and is clunky.

Putting the nation’s air-traffic control system into a nonprofit organization would help alleviate airline delays and cancellations, among other benefits, Robin Hayes, chief executive officer of JetBlue, wrote in an opinion piece published Thursday in Crain’s New York Business.

A proposal to partially privatize air traffic passed in the House, but wasn’t included in a final bill setting FAA policy this year after Senators objected.

According to the government delay numbers, it is the system the airlines have been so critical of that has improved the most.

From a high of almost 600,000 delays in 2007 blamed on the U.S. aviation system, the total fell to 316,684 last year. The total time that flights were late due to this category fell almost in half from 28.2 million in 2007.

One reason: The system has gotten better at adapting to weather that slows flights, which includes thunderstorms, fog, unusual winds and snow. Flights held up by weather caused about half of all minutes of delay in the early 2000s. That fell to less than one-third the past two years, according to the data.

Since 2008, most of the overall decline in tardy arrivals has been due to a reduction in the number of flights after bankruptcies and mergers, the introduction of new air-traffic technology and improvements in how the FAA’s controllers have adapted to thunderstorms in the summer months, according to John Hansman, a Massachusetts Institute of Technology aeronautics professor who has studied the issue.

It’s less clear why the delays attributed to airlines haven’t fallen with other categories, said Hansman and Vikrant Vaze, an assistant engineering professor at Dartmouth College who has also researched the subject. Airlines aren’t required to provide the government with underlying reasons they caused flights to be late.

“‘Air carrier delays’ — that category has been an enigma to me,” Vaze said.