Airline officials say the pilot thought the loud noises during the flight last month were due to cargo shifting, and in an internal memo they defended the crew.
A flight attendant on the April 20 trip said there was "a loud shaking noise from the belly of the plane." A few minutes later, there was another noise that "sounded like an explosion," the attendant said in an e-mail, according to Dallas television station WFAA.
The incident came to light because the flight attendants who heard the noise and felt the vibration believe their concerns were not taken seriously enough by the pilot, reports CBS News.
When the Boeing 767 landed safely in Paris after the nine-hour flight, ground crews discovered the panel about two feet by three feet and covering one of two air conditioners was gone.
In a statement, the airline said it was investigating the incident and wouldn't comment further.
"It was determined that at no time were crew or passengers at risk. The cabin never lost pressurization," the statement read.
Officials in the airline's flight department told pilots in a memo obtained by The Associated Press that the captain "did exactly what we want our captains to do."
"There was no way this crew could have known this panel had departed," said the memo from Jim Kaiser, American's manager of flight operations quality control, and Chuck Harman, the airline's fleet captain for Boeing 757 and 767 planes. "If they had known, they obviously would have returned" to DFW Airport.
According to the memo, no cockpit warning lights came on, and the pilot, who was not identified, also spoke to a maintenance technician in Fort Worth.
Kaiser and Harman, who are both pilots, said while pictures of the hole in the fuselage "are very dramatic," the passengers were never in danger.
A source at the airline, who spoke on condition of anonymity because he wasn't authorized to talk about the incident, said neither the captain nor other pilots who were on the flight as passengers noticed any unusual vibrations.
With a full load of fuel, the pilot would have been forced to circle DFW Airport while burning fuel, so he decided to keep heading toward the East Coast believing that he could make an emergency landing at any of several airports along the way, the official said.
Three hours into the flight, with no additional noises and the plane appearing to be burning fuel at a normal rate, the pilot decided the noise had probably been something shifting in the cargo hold, and he decided to continue across the Atlantic, the official said.
After the plane landed, a flight attendant snapped pictures of the missing panel, and the photos began circulating in e-mails between American Airlines employees.
Officials with the pilots' and flight attendants' unions did not immediately return messages for comment.
The incident on the Paris-bound flight occurred only a week after American canceled about 3,300 flights while it grounded its fleet of MD-80 jets to inspect electrical wiring.