All 379 people aboard the Japan Airlines (JAL) Airbus A350 managed to escape after it erupted in flames following Tuesday's crash with a De Havilland Dash-8 Coast Guard turboprop shortly after landing at Haneda airport.
But five died among the six Coast Guard crew who were due to depart on a flight responding to a major earthquake on Japan's west coast while the captain, who escaped the wreckage, was badly injured.
Authorities have only just begun their investigations and there remains uncertainty over the circumstances surrounding the crash, including how the two aircraft ended up on the same runway.
Experts stress it usually takes the failure of multiple safety guardrails for an plane accident to happen.
But transcripts of traffic control instructions released by authorities appeared to show the Japan Airlines jet had been given permission to land while the Coast Guard aircraft had been told to taxi to a holding point near the runway.
An official from Japan's civil aviation bureau told reporters there was no indication in those transcripts that the Coast Guard aircraft had been granted permission to take off.
The captain of the turboprop plane said he had entered the runway after receiving permission, a Coast Guard official said, while acknowledging that there was no indication in the transcripts that he had been cleared to do so.
"The transport ministry is submitting objective material and will fully co-operate with the... investigation to ensure we work together to take all possible safety measures to prevent a recurrence," Transport Minister Tetsuo Saito told reporters.
The Japan Safety Transport Board (JTSB) is investigating the accident, with participation by agencies in France, where the Airbus jet was built, and Britain, where its two Rolls-Royce engines were manufactured.
Japan Airlines says its plane burned for more than six hours after it crashed at Haneda airport. (AP PHOTO)
The JTSB has recovered the voice recorder from the coast guard aircraft, authorities said.
Meanwhile, Tokyo police are investigating whether possible professional negligence led to deaths and injuries, several media, including Kyodo and the Nikkei business newspaper, said.
Police set up a unit to investigate and planned to interview those involved, a spokesperson said, declining to say if they were examining suggestions of negligence.
Parallel investigations have raised concerns in the past over tensions between civil safety investigations and police-led inquiries.
"There's a strong possibility there was a human error," said aviation analyst Hiroyuki Kobayashi, who is a former JAL pilot.
"Aircraft accidents very rarely occur due to a single problem, so I think that this time too there were two or three issues that led to the accident."
In a statement on Wednesday, JAL said the aircraft recognised and repeated the landing permission from air traffic control before approaching and touching down.
All passengers and crew were removed within 20 minutes of the crash but the aircraft, engulfed in flames, burned for more than six hours, the airline said.
