An FAA inspector identified last week some airplane parts that did not have proper paperwork. It led the airline to temporarily ground 46 planes.
The agency said it has since determined that the parts do not present a flight risk.
The planes are currently being allowed to fly while the FAA continues to look at the paperwork issues and the parts supplier.
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The federal agency said it's too early to say whether Southwest could face fines for the incident.
"Safety is the No. 1 priority at Southwest, so we are staying very open and connected to everyone involved as we work to resolve this,” a Southwest spokesperson said.
The part involved, an "exhaust gate assembly hinge fitting,” basically protects the flaps from excessive heat from the engines.
The FAA said Southwest's supplier manufactured the parts instead of buying them from an approved manufacturer.