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 .
Woman picks up wrong bag with gun belonging to pilot , officials say . Gun belonged to a JetBlue Airways pilot authorized to carry it under TSA program . Two flights delayed about an hour due to the mix-up , airline says . TSA says the pilot `` has been relieved of his firearm '' pending an investigation .