The "accidental discharge" Saturday aboard Flight 1536 from Denver, Colorado, to Charlotte, North Carolina, did not endanger the aircraft or the 124 passengers, two pilots and three flight attendants aboard, said Greg Alter of the Federal Air Marshal Service.
"We know that there was never any danger to the aircraft or to the occupants on board," Alter said Monday.
It is the first time a pilot's weapon has been fired on a plane under a program created after the Sept. 11, 2001, terrorist attacks to allow pilots and others to use a firearm to defend against any act of air piracy or criminal violence, he said.
The federal Transportation Security Administration is investigating how the gun discharged and is being assisted by the Air Marshal Service, Alter said. Officials did not say where the bullet hit.
The service declined to release additional details.
Federal Aviation Administration spokesman Mike Fergus said his agency is also investigating to make sure that the plane is safe. The Airbus A319 has been removed from service, the airline said.
The TSA initially opposed the Flight Deck Officer program to arm and train cockpit personnel. Agency officials worried that introducing a weapon to commercial flights was dangerous and that other security improvements made it unnecessary. Congress and pilots backed the program.
"The TSA has never been real supportive of this program," said Mike Boyd, who runs the Colorado-based aviation consulting firm The Boyd Group. "It's something I think Congress kind of put on them."
Pilots must volunteer, take a psychological test and complete a weeklong firearms training program run by the government to keep a gun in the cockpit.
Boyd said he supports the program to arm pilots, saying, "if somebody who has the ability to fly a 747 across the Pacific wants a gun, you give it to them." But he said Saturday's incident could have been much worse.
"If that bullet had compromised the shell of the airplane, i.e., gone through a window, the airplane could have gone down," he said.