(CNN) -- Southwest Airlines said it resumed normal operations Thursday after several dozen planes were reinspected on Wednesday.
"We had a normal launch today," Linda Rutherford, a Southwest vice president for public relations and community affairs, said in a statement to CNN.
There were three flight cancellations Thursday, unrelated to the inspections.
The company pulled 44 planes from service for inspection after an "ambiguity related to required testing" was found during a review of records, the airline said Wednesday.
The 44 aircraft included five that were already out of service for scheduled maintenance checks, plus one that "was already retired," the company said.
Southwest canceled about 4 percent of Wednesday's flights when it took the other 38 planes out of service, the release said.
But good weather conditions helped minimize the schedule disruptions, Southwest said, and flights ran more than 90 percent on time Wednesday.
The company said more service interruptions could happen in the coming days because of "the ongoing internal review of Southwest's maintenance programs, policies, and procedures."
The FAA has said Southwest operated 46 Boeing 737s on nearly 60,000 flights between June 2006 and March 2007 while failing to comply with an FAA directive requiring repeated inspections of fuselage areas to detect fatigue cracking.
The FAA also alleges that after Southwest discovered it had failed to comply, it continued to operate the same planes on an additional 1,451 flights in March 2007.
Documents provided to CNN show that another 70 Southwest jets were allowed to fly past the deadline for mandatory rudder inspections.
Neither the release nor Southwest spokeswoman Whitney Eichinger said whether the inspections were of the plane's fuselages or rudders.
The House Transportation and Infrastructure Committee issued a statement on Southwest's decision to ground the 38 planes.
"This action by Southwest Airlines raises serious questions about whether [the Federal Aviation Administration] adequately followed up on the discovery a year ago that Southwest had failed to make required inspections," the statement said.
"FAA should have immediately undertaken a review of the airline's records to see whether Southwest had conducted all required inspections, and whether procedures were in place to ensure timely inspections in the future.
"Had such a review been conducted, FAA would have found or prevented the 'ambiguity' in Southwest's maintenance which Southwest has discovered after its own review of its records this week."
According to detailed congressional documents obtained by CNN, the FAA initiated actions to seek a $10.2 million civil penalty against the airline for allegedly operating 46 airplanes without conducting mandatory checks for fuselage cracking.
Rutherford said the inspections take about 90 minutes.
Earlier this week, Southwest placed three employees on administrative leave and began conducting an internal investigation into the allegations that it flew planes without proper inspections.
"Upon learning last month of an investigation with respect to our handling of this inspection and an airworthiness directive, I immediately ordered an independent and comprehensive investigation by outside counsel," Southwest Airlines CEO Gary Kelly said in a statement released Tuesday. E-mail to a friend
CNN's Drew Griffin contributed to this report.