Japan’s transport authorities have begun inspecting the charred remains of a passenger jet and a coast guard plane that collided at a Tokyo airport.

All 379 people on board the Japan Airlines (JAL) Airbus A350 had a miraculous 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 responding to a major earthquake on the west coast, while the captain, who escaped the wreckage, was badly injured.

Japanese authorities say the cause of the crash is unclear.

The Japan Safety Transport Board (JTSB) is investigating the incident, with participation by agencies in France, where the Airbus aeroplane was built, and Britain, where its two Rolls-Royce engines were made, people familiar with the matter said.

Officials examine the burnt wreckage of the Japan Airlines passenger plane on the tarmac. Photo: AFP/Getty

The JTSB has recovered flight and voice recorders from the coast guard aircraft, Kyodo news agency said.

Tokyo police are investigating whether possible professional negligence led to deaths and injuries, several media outlets said.

Police set up a special unit at the airport to investigate the runway and planned to interview those involved, a spokesperson said, but declined to say if they were examining the negligence concerns.

“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.”

At a series of press conferences since the crash, officials and airline executives have been asked what information crew received from traffic control and why both planes ended up on the same runway.

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 evacuated within 20 minutes of the crash, but the aircraft, engulfed in flames, burned for more than six hours, the airline said.

The JAL plane was told to continue its approach to runway 34R at 5.43pm local time, and was given clearance to land at 5.45pm.

That was two minutes before authorities say the collision occurred on the same runway at 5.47pm, according to air traffic control recordings posted at liveATC.net.

“Clear to land 34R Japan Airlines 516,” a controller can be heard saying in one recording, referring to the passenger jet by its flight number.

The Coast Guard has declined to comment on the circumstances of the crash.

The plane, one of six Coast Guard aircraft based at the airport, had been due to deliver aid to regions hit by Monday’s earthquake of magnitude 7.6 that has killed 64, while survivors face freezing temperatures and prospects of heavy rain.

The accident forced the cancellation of 116 domestic, and four international, flights on Wednesday, the government said.

But emergency flights and high-speed rail services were helping to ease the congestion, chief cabinet secretary Yoshimasa Hayashi told reporters.

-Reuters