(CNN) -- Southwest Airlines was inspecting 44 planes Wednesday after an "ambiguity related to required testing" was found during a review of records, the airline said.
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.
The House Transportation and Infrastructure Committee, which initiated an investigation months ago, issued a statement on Southwest's decision.
"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.
The FAA should have "immediately undertaken a review of the airline's records."
"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," the committee statement said.
The 44 planes included five that were already out of service for scheduled maintenance checks plus one that "was already retired," the company said in a news release Wednesday afternoon. Watch what's to be expected »
Taking the other 38 planes out of service for inspection resulted in the cancellation of "approximately 4 percent of today's Southwest flights," the release said.
"Due to good weather conditions, the decision caused minimal schedule disruptions and the airline is running more than 90 percent on time," it said.
By midafternoon, it said, "a portion of the aircraft have been inspected, cleared, and returned to service. The airline expects to have all of these aircraft inspected by early this evening."
It said other such service interruptions could occur in coming days because of "the ongoing internal review of Southwest's maintenance programs, policies, and procedures."
Linda Rutherford, another Southwest spokeswoman, said the inspections take 90 minutes.
Southwest Airlines CEO Gary Kelly said in a statement released Tuesday: "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 did not say whether the inspections were of the plane's fuselages or rudders, both of which were mentioned in a CNN exclusive investigation released last week.
According to detailed congressional documents obtained by CNN, Southwest Airlines flew some planes in violation of mandatory safety checks.
Last week the Federal Aviation Administration 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.
The amount of the proposed penalty "reflects the serious nature of those deliberate violations," the FAA said in a statement.
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. The airline later found that six of the 46 planes had fatigue cracks, the FAA said.
Documents provided to CNN show that another 70 Southwest jets were allowed to fly past the deadline for the mandatory rudder inspections. Those documents also say that 47 planes -- one more than reported by the FAA -- flew without their mandatory fuselage inspections.
In some cases, according to the documents the FAA provided to congressional investigators, the planes flew for 30 months past government inspection deadlines and should have grounded them until the inspections could be completed.
The documents were prepared by two FAA safety inspectors who have requested whistle-blower status from the House Transportation and Infrastructure Committee. Both inspectors have been subpoenaed to testify before the committee.
Rep. James Oberstar, D-Minnesota, who heads the committee and who has called the situation "one of the worst safety violations" he has ever seen, is scheduled to hold a hearing April 3 to ask why the airline may have allegedly put its passengers in danger.
The whistle-blowers say FAA managers knew about the lapse in safety at Southwest, but decided to allow the airline to conduct the safety checks on a slower schedule because taking "aircraft out of service would have disrupted Southwest Airlines' flight schedule."
"I am concerned with some of our findings as to our controls over procedures within our maintenance airworthiness directive and regulatory compliance processes," Kelly said Tuesday. "I have insisted that we have the appropriate maintenance organizational and governance structure in place to ensure that the right decisions are being made."
In addition to putting three employees on administrative leave, Southwest has hired a consultant to review its maintenance program controls and is working closely with the FAA on its current audit of the fleet.
"These are important and necessary steps," Kelly said. "We have been a safe company. I believe we are a safe company. I am committed to making sure we become safer still."
The mandatory checks for fuselage cracks were required after the cabin of an Aloha Airlines 737 tore apart in midair in 1988, killing a flight attendant. The incident was blamed on cracks in the fuselage that grew wider as the plane underwent pressure changes during flight.
Southwest Airlines has never had a catastrophic crash. E-mail to a friend
CNN's Drew Griffin contributed to this report.