A Delta Air Lines passenger carried a loaded gun by accident through airport security in Atlanta earlier this month and took it on a flight to Japan, officials with the Transportation Security Administration said.

The passenger later discovered the firearm and alerted the authorities, who met the plane when it landed on Jan. 3 in Tokyo, officials said. The gun was taken through a T.S.A. checkpoint at Hartsfield-Jackson International Airport in Atlanta on Jan. 2, the 11th day of the partial federal government shutdown, as concerns were growing that security agents, who are working without pay, might not show up.

But a T.S.A. spokesman, Michael Bilello, insisted on Monday that the shutdown was not to blame for the security breach and that the gun was undetected because “standard procedures were not followed.” About five percent of T.S.A. employees nationwide did not report to work on the day of the flight, Wednesday, Jan. 2, which was the identical rate of unscheduled absences on Wednesday, Jan. 3, 2018, Mr. Bilello said.

He said the agency did not release staffing rates for individual airports and would not specify what “standard procedures” were not observed. There are 51,000 airport security agents nationwide.