But more broadly, the turmoil is better understood as a reaction — or overreaction, in the eyes of some in the industry — to a long-term shift, over two presidencies, in the way the F.A.A. oversees the airlines.  In the 1990s, the agency was more of a cop on the beat, handing out penalties to those who broke the rules.  “You used to fear an F.A.A. inspector showing up,” said Joseph Tiberi, a spokesman with the International Association of Machinists and Aerospace Workers. “They checked everything from the nuts and bolts in your tool kit to the paperwork in the cockpit.”  But then a different, more collaborative approach emerged that critics say went too far. After the 2001 terrorist attacks, which crippled the industry, the agency began “a creep away from their rigorous oversight of maintenance,” said Representative James L. Oberstar, Democrat of Minnesota and the chairman of the House committee that has pushed the issue.  That arrangement was “coddling the airlines,” he added, which eased the burden on the F.A.A., with its inspectors spending more time on paperwork than on airplanes.  The change began after the T.W.A. 800 and ValuJet disasters in the mid-1990s, when regulators and the industry convened a “safety summit.” Then the Clinton administration formed a national commission in 1997 on aviation safety and security, led by Vice President Al Gore and known as the Gore Commission. It set a goal of cutting the rate of fatal accidents 80 percent over 10 years.  One idea was for the F.A.A. to start working more closely with the industry. If airlines shared their mistakes or problems without fear of retribution, the reasoning went, the system would benefit from these shared lessons.  And it seems to have. Over the next decade, the accident rate fell 65 percent, and this new approach is widely seen as having played a role in the drop.  Then the F.A.A., under the Bush administration, took on a role after the Sept. 11 attacks to help the industry recover — “through technology, through greater efficiencies, through sensible and non-burdensome regulatory schemes,” Marion C. Blakey, the F.A.A. administrator in 2002, said at the time. She declined to be interviewed for this article.  This more collaborative approach was reflected in a “customer service initiative” announced by the F.A.A. in April 2003.  The customers in this case were not passengers; they were the airlines the F.A.A. regulates. The core principles of the new initiative, which inspectors could print up on pocket-size cards, included creating for the airlines “an environment without fear of retribution if you challenge our decisions” and “clear guidance on how you can elevate your concerns to the next higher level of authority.”  The F.A.A.’s watchdog role, to many Democrats in Congress who now oversee airline regulators, grew toothless. “We had drifted a little bit too much toward the over-closeness and coziness between regulator and regulated,” said H. Clayton Foushee Jr., a former F.A.A. official who led a recent inquiry by Mr. Oberstar’s committee.  Some inspectors in the field were also concerned by the drift. In early 2003, Charalambe Boutris, an inspector in the F.A.A.’s Dallas office, began reviewing Southwest’s engine maintenance records.  The task would seem the equivalent of the Maytag repairman’s job, since Southwest has a stellar safety record. But Mr. Boutris discovered the airline’s record-keeping was inconsistent and varied from aircraft to aircraft, according to the United States Office of Special Counsel, which reviewed his accusations.  After raising the issue with a supervisor, Mr. Boutris was told he could send Southwest a letter expressing concern, but not a more serious “letter of investigation,” which is what regulations called for under such circumstances.  He continued to find problems with the airline’s record-keeping, and again pressed for an investigation. But his supervisor again chose a slap-on-the-wrist letter, and Southwest officials began to lobby for Mr. Boutris’s removal.  Yet problems remained. In January 2007, the airline discovered cracks on some of its Boeing 737s. Less than two months later, an unidentified whistle-blower in the F.A.A.’s Chicago office noticed a crack in a Southwest jet that had been flown the day before.  Earlier this year, Southwest told the F.A.A. that it had flown 46 planes without the required inspections of fuselage panels, operating the defective planes for up to nine months on more than 61,000 flights. That “self-disclosure” normally would have allowed Southwest to avoid financial penalties as long as it fixed the problems. And it kept flying the planes.  It also flew 27 planes that were not in compliance with an F.A.A. directive requiring inspections of cargo doors.  Before the House Transportation and Infrastructure Committee hearings on April 3, Mr. Boutris and another inspector, Douglas Peters, testified about being told by supervisors to ignore violations by Southwest. “My supervisor was suppressing my authority and responsibility to report them in accordance with mandated F.A.A. guidance,” Mr. Boutris testified.  The two men, who say they have received threats over their decision to expose the airline, have become “rock stars” within aviation safety circles, Mr. Foushee said.  Mr. Foushee said he began to hear “noise” as soon as he joined the committee in January 2007 about the relationship between the airlines and the agency.  “F.A.A. people would call me, and contact me, saying, ‘We’re not able to do our jobs anymore,’ ” said Mr. Foushee, who worked for a law firm in Washington before joining the committee staff.  He spoke first with Mr. Peters, who contacted him anonymously. He then spoke with Mr. Boutris and began the committee’s investigation into the conduct of the airlines and the agency.  The two men “turned over incontrovertible evidence that what happened happened,” he said.  When the committee began circulating a damning report on how the agency had treated the two whistle-blowers, written by the Special Counsel’s office, the F.A.A. decided it had to act. It ordered a nationwide audit and relieved Mr. Boutris’s supervisor of his safety responsibilities.  Now the F.A.A. is conducting a broad national audit, which led to the grounding of all MD-80s in the American Airlines fleet. More groundings of other planes throughout the industry are likely to occur in coming weeks as the audit continues. American, for its part, said it would resume its normal schedule on Sunday.  More disclosures about lax inspections are likely, Mr. Oberstar said.  “There are more people coming to us with reports of stuff,” he added. “They said, ‘No one was listening to us for last six or seven years; now we’ve got someone who understands the problems, understands the safety implications.’ ”  He said the new reports came from all around the country, not just the regional office responsible for Southwest Airlines.  “Pilots talk to me, flight attendants talk to me, ramp mechanics have stopped me and said, ‘I want you to know this is happening,’ ” Mr. Oberstar said.  A number of industry officials, however, call the latest crackdown an overreaction, pointing to American’s decision to park all 300 of its MD-80s while it checked whether their wiring complied with a safety directive.  One senior executive at another airline, who spoke on the condition of anonymity, said the agency’s new stance reflects the new tone in aviation safety.  “In the past, you wouldn’t have grounded the whole fleet,” the executive said. “There’s a question of what’s rational and what’s not.”  A change in procedures seems likely. Tom Brantley, president of the Professional Aviation Safety Specialists, the inspectors’ union, testified on April 3 that inspectors have been defanged by the F.A.A. itself.  For example, he said, if the inspectors show up without warning, he said, airlines would complain to their F.A.A. superiors that “they’re slowing us down, they’re asking people questions, they’re costing us money.”  And the agency seems likely to change its procedure for “self-reporting” and avoiding penalties. Two F.A.A. managers have been transferred, and others may lose their jobs.  Passengers will have to endure more canceled flights in coming weeks. But they are also left to make sense of mixed signals — about planes that rarely crash anymore but whose safety is suddenly in doubt, and about an agency that was long considered best-in-class that suddenly seems broken.  The unraveling relationship between the F.A.A. and the airlines is “like a divorce,” said James E. Hall, a former chairman of the National Transportation Safety Board. “And the children are the passengers.”  Mr. Oberstar said these were “difficult times for the passengers,” with, by his count, 568 aircraft grounded so far. “But I think they’d rather be on the ground than 7 miles in the air, with no way to pull over to the curb and check under the hood,” he said.  Matthew L. Wald reported from Washington, and Micheline Maynard from Detroit.  A version of this article appears in print on , on Page A1 of the New York edition with the headline: Behind the Chaos in Air Travel, a Pendulum Swing at the F.A.A. Order Reprints| Today's Paper|Subscribe
A current safety crackdown is a shift away from what critics say was the agency’s coddling of the airlines.