The agency said in a statement that the security breach was not due to the partial government shutdown.
A man traveling from Atlanta to Japan earlier this month was able to carry a gun through a security checkpoint and onto a Delta Air Lines flight, according to the Transportation Security Administration.
The unidentified passenger boarded a plane on Jan. 2 at Hartsfield-Jackson Atlanta International Airport with his firearm, the TSA said in a statement. The agency did not say if the gun was loaded.
The man alerted airline workers once he arrived at Tokyo Narita International Airport who in turn told the TSA, Delta Air Lines said.
Officials said the passenger "was fully cooperative with authorities."
TSA said in a statement that the security breach was due to "standard procedures" not being followed, and dismissed the idea that it was related to workers calling out because of the shutdown, which entered day 24 on Monday.
The agency, which is part of the Department of Homeland Security, is among those federal workers affected by the shutdown.
"There was not a staffing issue as some are speculating," the agency said, adding that the national callout rate for Jan. 2 was the same as it was a year ago when there wasn't a shutdown. "The ATL checkpoint lane was fully staffed."
"TSA has held those responsible appropriately accountable," the agency's statement continued.
While TSA has said the partial government shutdown is not responsible for the breach, the shutdown has affected how various airports across the nation are being staffed.
George Bush Intercontinental Airport in Houston said in a tweet Monday that because of staffing issues related to the shutdown the TSA checkpoint and ticketing counter in Terminal B would be closed. It's not immediately clear when the checkpoint will open.
Houston's airport is ranked among the top 20 in the world for its number of take-offs and landings, according to a 2018 report by the Airports Council International.
"Flights scheduled to depart from Terminal B will operate as normal," the statement read. "Passengers with flights scheduled to depart from Terminal B are being directed to the ticket counters and TSA checkpoints located in Terminal C and Terminal E."
The closure follows a similar move at Miami International Airport in Florida, which closed a TSA checkpoint on Jan. 12 "due to the federal funding lapse," the airport said in a tweet. The checkpoint returned to normal operation on Monday.