An All Nippon Airways plane flew 1,600 meters higher than instructed by air traffic controllers for about 40 minutes during a flight from Nagasaki to Tokyo this month due to an altimeter adjustment error.
ANA said Tuesday it reported the incident to the Land, Infrastructure and Transport Ministry even though the Boeing 767, with 96 people on board, apparently did not come close to other planes.
Ministry officials said a warning would be delivered to ANA.
ANA grounded the captain and copilot and has temporarily removed three ground employees from their duties.
"It was a very serious incident that should never have happened. We will try not to repeat such an error," Mitsuo Morimoto, an ANA executive in charge of flight operations, told a news conference.
About 10 minutes after ANA Flight 664 took off from Nagasaki Airport at 11:12 a.m. June 5, the altimeter on the captain's side and the one on the copilot's side showed different figures, ANA officials said.
The altimeters were calculating altitude using different measuring devices and the one on the copilot's side had an incorrect figure, but the 39-year-old captain switched his altimeter to reflect the copilot's data even though he meant to switch to data from a third measuring device, ANA said.
As a result, the two altimeters showed the plane was at 8,800 meters, even though it was at 10,400 meters. The captain said he didn't see other planes while flying at the incorrect altitude, ANA said.