The man, later identified as a convicted felon, ran with the gun from the checkpoint and escaped out an airport exit, the Transportation Security Administration said. Authorities said it was not an active shooter incident and described the discharge as accidental.
Police said later they had issued a warrant for the arrest of the passenger, 42-year-old convicted felon Kenny Wells.
"Never in my life, never in my life have I experienced that before," said one traveler from North Carolina who was in the airport during the incident.
WATCH: Accidental gunfire incites panic at US' busiest airport
The airport's police commander, Maj. Reginald Moorman, said Wells was being sought on charges including carrying a concealed weapon at a commercial airport, possession of a firearm by a convicted felon, discharging a firearm and reckless conduct.
"We are actively pursuing this individual as we speak," Moorman said at a news briefing Saturday evening with TSA and airport officials.
The discharge caused a frenzy on social media as alarmed travelers posted videos to Twitter and other online sites showing and describing moments of chaos and confusion at Hartsfield-Jackson Atlanta International Airport, one of the nation's busiest. A commuter rail link to the airport also was briefly halted as a precaution.
Authorities said three people suffered minor injuries, including one person who fell in the airport's atrium area away from the checkpoint, and two complaining of shortness of breath.
No one was shot, a TSA executive added.
"We were fortunate that when the firearm went off, no one was seriously injured," Robert Spinden, the TSA's director of federal security for Georgia, said at the airport briefing. Officials didn't immediately disclose the type of weapon involved.
Social media users reported there were long lines for security and missed flights for some. The incident came ahead of the peak Thanksgiving holiday travel season as people are still coping with the frustrations and concerns of safely traveling during the ongoing COVID-19 pandemic.
Although the FAA ordered a temporary ground stop, airport officials said operations never ceased and the airport didn't close. They said the airport returned to normal operations in under two hours.
The TSA statement said it all began when the passenger was about to undergo a bag search by an official at 1:30 p.m. at the airport's main checkpoint after an X-ray scan detected what was described as a "prohibited item."
"He advised the passenger not to touch the property, and as he opened the compartment containing the prohibited item, the passenger lunged into the bag and grabbed a firearm, at which point it discharged. The passenger then fled the area," according to the statement.
The Atlanta Journal-Constitution reported social media users rushed from the airport in the chaos after hearing the gun going off. One video posted on Twitter showed people running out of the terminal, some anxiously glancing back or watching in apparent confusion.
After Atlanta police gave the all-clear normal operations resumed at the airport before 3:30 p.m. TSA said all passengers had to be re-screened.
The TSA said the incident underscores the importance for all passengers of checking personal belongings for dangerous items before leaving for the airport. Passengers caught with firearms at airport checkpoints face a civil penalty. The TSA says firearms may be allowed in checked baggage when they are unloaded and packed in a locked, hard-sided case.
Last month, federal officials reported a spike in firearm seizures at Atlanta's airport - part of a record year for the number of guns detected at airport security checkpoints.
The TsA said it seized 391 firearms at Hartsfield-Jackson airport in the first nine months of 2021. That's up from 220 last year when passenger counts were down significantly because of the pandemic. But it's also a big jump from 2019, when 323 firearms were seized in Atlanta.
Across the nation, the TSA said, it had stopped 4,495 airline passengers from carrying firearms onto their flights by Oct. 3 of this year, surpassing the previous record of 4,432 firearms caught at checkpoints in all of 2019.
The agency announced the 2021 figures in a news release and noted the record came despite a continued dip in passengers because of the pandemic. The release did not offer an explanation or theory about the spike in gun seizures.
Hartsfield-Jackson is one of the nation's busiest airports, though other U.S. airports rival its passenger screening numbers. Dallas Forth Worth International Airport was second on the TSA's list, with 232 firearms seized by Oct. 3.