A transcript of communications released by the ministry last week suggested that the JAL plane was cleared to land, but the coast guard plane was instructed to halt before the runway.
Controllers told the coast guard plane that it was “No 1”, meaning next in line for take-off.
But the coast guard pilot – the only survivor – has reportedly said he believed he had clearance to move onto the runway, where his plane stood for around 40 seconds before the crash.
The charred wreckage of both planes were cleared from the tarmac at Haneda, and flight operations have returned to normal, with extra staff working at the airport’s control tower since Saturday.
A dedicated staff member has also been watching the warning system at Haneda since the weekend.
“Control centre staff have to monitor various things and can’t simply stare at the warning system,” a transport ministry official in charge of aviation affairs explained to AFP.
In the decade to 2023, at least 23 “serious incidents” that risked a runway collision were reported by the Japan Transport Safety Board, according to the Asahi newspaper.
In five of the cases, mistakes in air traffic control were suspected as a cause, the newspaper said.