"Even though it was successfully accommodated, it's an issue of why did they get to that situation to begin with?" Allen said. "That is where we have to be vigilant to look at these systemic issues so they don't manifest themselves into accidents and incidents."
American insists the comprehensive audit was prompted by last year's congressional hearing and not by any particular problems since then. The carrier says it has performed well on recent regulatory exams and has added members to its audit team since last year.
"We think our team is ready, and we're cooperating with" the FAA, said Bob Reding, American's executive vice president of operations.
Southwest went through a similar examination last year. The FAA discovered problems that Southwest agreed to fix in exchange for paying a fine of $7.5 million, down from $10.2 million, the FAA said.
The changes required Southwest to rewrite all of its FAA-approved manuals and to increase its regulatory compliance staff.
Mike Van de Ven, Southwest's chief operating officer, said the company already planned to make some of the changes. Southwest has added nearly 20 people to its maintenance team to help comply with FAA demands, he said.
"I don't feel Southwest needs the FAA as a regulator to look over us and tell us we're safe enough," Van de Ven said. "We have all the reasons to be as safe as we possibly can, because safety is our number one priority."
Questions persist over how airlines perform work required by airworthiness directives. Many airlines complain that the orders are so complex they require flexibility to incorporate into a carrier's maintenance practices.
The FAA acknowledges the tension over safety directives and is preparing a report that will provide guidance to inspectors who are grappling with how serious a violation is, Allen said.
Basil Barimo, vice president of operations and safety for the Air Transport Association, said the report would urge that newly issued airworthiness directives distinguish between work that is safety-critical and work that isn't.
"It's going to provide a flow chart, if you will, and a process to help our inspectors not be black and white, but be more understanding of the nuances and who to reach out to," Allen said.
Still, carriers are worried about FAA enforcement and are seeking far more retroactive approvals for work that doesn't meet the exact specifications of airworthiness directives.
American and Southwest have sought far more of these approvals -- known as an "alternate means of compliance," or AMOC -- since last year's upheaval.
According to the FAA, American received 47 AMOCs between April 1, 2008 and March 31, compared with seven over the same period a year earlier. Southwest received 68 AMOCs over the past year, compared with 16 a year earlier.
"In the past, [airlines] would have said, 'this is a minor issue. We determine ourselves, in collaboration with our local FAA, that it's not a significant deviation and therefore we don't need to get some special approval,'" Barimo said.
American officials say they've received a disproportionate amount of FAA scrutiny because their maintenance is performed within the country. Many competitors have outsourced heavy maintenance to foreign repair stations, which the FAA inspects infrequently, according to the U.S. Department of Transportation's inspector general.
American has 12,000 aviation mechanics, and Southwest has 1,700. That means American will inevitably report more mistakes through regulatory programs that encourage airline employees to report errors in exchange for immunity from enforcement action.
In February, the airline reported through such a program that it improperly performed work related to an airworthiness directive issued in 2006. The order governed how thrust reversers are maintained on Boeing 777 airplanes.
Regulators are now investigating how long American operated the planes out of compliance before disclosing it to the FAA in mid-February, officials said.
American's Wagner declined to discuss the investigation, but said the carrier is "as proactive as we can possibly be in addressing safety issues in the fleet."
In the face of unprecedented federal scrutiny of airline maintenance, airlines are taking dramatic steps to prove compliance, including canceling flights to redo work they may have already performed.
Whistleblowers say officials looked the other way.
The audit, which applies to all US carriers, wraps up this week. The FAA could announce results as soon as Monday.