The airline said the JAL flight crew agreed to allow the landing.
“The aircraft's notification system malfunctioned during take-off,” the airline said in a press release.
367 passengers and 12 crew members were evacuated when the plane collided with a Japan Coast Guard aircraft while landing at Haneda Airport in Tokyo.
The airline described the moments before and during the landing, saying all three crew members in the cockpit were cleared to land. Eight children were on board the Airbus A350.
All exited the plane via three emergency exits, the airline said. Passengers “successfully made an emergency evacuation” as the plane caught fire, the airline said.
At least 14 passengers have sought medical advice. One person suffered bruising and 13 people sought counseling “due to physical discomfort,” the airline said.
Flight JAL516 took off on time from New Chitose Airport in Sapporo, Japan at around 3:50pm on Tuesday. Japan Airlines said it “did not encounter any problems or irregularities” during take-off or during the flight. Landed late at 5.47 pm
“According to interviews with the operations team, they acknowledged and repeatedly approached landing clearance from air traffic control, then proceeded with the approach and landing procedures,” Japan Airlines said in a statement.
The plane struck a Japan Coast Guard aircraft, killing five of its six crew members, Japanese officials said. Footage from the scene showed the large plane burst into flames as it taxied down the runway.
The Airbus was declared a total loss after it caught fire on the runway, the airline said.
The aircraft, registered as JA13XJ, was delivered to Japan Airlines on November 10, 2021, Airbus said in a statement on Tuesday. Rolls Royce Trent XWB engines powered the aircraft.
The French plane maker said it was sending a “team of experts” to Japan to assist French and Japanese investigators probing the crash.
ABC News' Will Gretzky and Clara McMichael contributed to this story.