The FAA imposed a $10.2 million civil penalty on Southwest this month for missing the inspections and then continuing to fly the planes with passengers on board even after realizing the mistake. Southwest officials have said they repaired small cracks in the fuselages of six planes last year and four this month.
The FAA said it would check compliance with at least 10 safety orders at every U.S. airline by Friday. A more complete audit is due by the end of June.
The airlines declined to detail how much they were losing on canceled flights and extra inspections and maintenance.
Although thousands of passengers were inconvenienced over the past two days, analysts downplayed any notion that the cancellations would hurt the airlines financially. They said the costs would pale in comparison to high fuel prices.
Delta expected to cancel about 275 flights nationally, or about 3 percent of its schedule, before returning to normal operations early Friday, said spokeswoman Chris Kelly.
American, the nation's largest airline, canceled 141 flights by mid-afternoon Thursday, or about 6 percent of its estimated 2,300 flights, officials said. The Fort Worth-based airline canceled 318 flights Wednesday.
At American, inspectors from the airline and the Federal Aviation Administration focused on fixing the spacing between cords used to secure bundles of wires in the auxiliary hydraulic systems of its MD-80 aircraft.
"In no way was safety compromised, but the (FAA) directive said 'Do it this way,"' said American spokesman Tim Smith.
American completed inspections and in some cases alterations on 269 MD-80s by mid-afternoon, and another 21 were still undergoing work that was expected to be done Thursday, Smith said. Nine planes remained to be inspected Thursday night, he said.
Smith said American found seats for most passengers on other planes but also put some customers on other airlines' flights.
The largest number of cancellations, 42, were departures from Dallas-Fort Worth International Airport, Smith said. Flights from that airport and O'Hare are more likely to use MD-80s, while some airports, such as Miami, were barely affected, he said.
Delta expected heavy volumes Thursday at its hub at Hartsfield-Jackson Atlanta International Airport, Kelly said. Both Delta and the Transportation Security Administration were bringing in extra staff to handle the crowd of travelers, she said.
"I don't think it's a huge deal," said James Higgins, an airline analyst with Soleil Securities. "In the scheme of things, with oil doing what it's been doing, I don't think it will be meaningful."
Separately, Delta raised its fuel surcharge by $10 per round trip. Delta rolled back a similar increase last week when some other airlines declined to match it, keeping their fares lower.
Michael Derchin, an analyst at FTN Midwest Securities, said it was important for the airlines to explain the cancelations if they want to limit the fallout.
"Safety is the number one item for any airline, so they want to make sure people understand they're taking all the necessary steps," Derchin said. "It's worth it to them to take these planes out quickly and get any issues resolved quickly."
Shares of American parent AMR Corp. fell 23 cents, or almost 3 percent, to $8.38; and shares of Delta Air Lines Inc. lost 39 cents, or 4.5 percent, to $8.35. For AMR, the closing price was a 52-week low, and Delta shares hit a 52-week low of $8.34 during the session.
The Associated Press contributed to this report.