Authorities have begun investigating and there are still uncertainties about the circumstances of the incident, including how the two planes ended up on the same runway.
However, transcripts of traffic control instructions released by authorities appear to show that the Japan Airlines plane was given permission to land, but the Coast Guard plane was instructed to taxi to a stopping point near the runway.
An official from Japan's Civil Aviation Authority told reporters that there was no indication in those logs that the coast guard plane had been given clearance to take off.
The captain of the Coast Guard plane said he entered the runway after receiving permission, a Coast Guard official said, but acknowledged there was no indication in the logs that he had the authority to do so.
“The Ministry of Transport is submitting objective material and will cooperate fully in the investigation to ensure that we work together and take all possible security measures to prevent something like this from happening again,” Transport Minister Tetsuo Saito told reporters.
Japan's transport safety committee is investigating the incident, involving authorities in France, where the Airbus plane was built, and the United Kingdom, where the RollsRoyce engines were made, people familiar with the matter said.