Washington (CNN) -- Transportation Security Administration officials are investigating an incident this week in which a traveler apparently unintentionally picked up the wrong bag and boarded an airplane -- not knowing the bag had a gun belonging to an armed pilot.
Thursday morning's incident at New York's John F. Kennedy International Airport resulted in the delay of two flights, the hourlong closure of an airport checkpoint and an ongoing TSA investigation, officials said.
The gun belonged to a JetBlue Airways pilot who was authorized to carry it under the TSA's Federal Flight Deck Officer program, which trains airline pilots in the use of handguns and authorizes them to use them in jet cockpits to deter hijackers.
The firearm "was properly secured in a fashion that rendered it incapable of being discharged," TSA spokesman Nick Kimball said.
Persons familiar with the investigation said a woman apparently picked up the bag at the airport gate and boarded a flight to Fort Lauderdale, Florida, while the pilot who owned the bag was getting on his flight to Pittsburgh. Before her plane departed, the woman realized she had the wrong bag and gave it to the plane's flight crew, who looked inside and saw the pilot's identification.
While the exact circumstances are unclear, a source said, the bag was returned to JetBlue, and it was found to contain the pilot's firearm. At that point, the Port Authority of New York and New Jersey police were contacted, the source said.
A JetBlue spokeswoman Jenny Dervin said two flights were delayed about an hour because of the mix-up and that another pilot was assigned to fly the plane to Pittsburgh to avoid further delay.
The TSA said Friday the pilot "has been relieved of his firearm" pending the investigation.
Pilots who join the TSA program do so voluntarily, and are not compensated by the government for their security services.
In 2008, a US Airways pilot was fired after accidentally discharging his handgun in the cockpit while a plane was flying at 8,000 feet on approach to Charlotte, North Carolina. The bullet penetrated the fuselage but did not damage any crucial instruments or wiring.
The incident apparently occurred while the pilot was attempting to secure the gun during the fight's landing phase, which was in violation of TSA rules.
CNN producer Mike M. Ahlers contributed to this report.