All 379 people on board the JAL Airbus A-350 widebody jet on Tuesday escaped before the plane was completely engulfed in flames that took more than six hours to extinguish.
But five of the six crew of the other aircraft - a smaller Coast Guard plane that had been on its way to deliver aid to quake-hit regions on Japan's west coast - were killed, with the surviving pilot badly injured.
A Japan Airlines plane was destroyed when it hit another aircraft at Tokyo's Haneda airport. (AP PHOTO)
As investigators combed the charred wreckage on Thursday, transport authorities are probing the circumstances that led to the Coast Guard plane entering the runway where the passenger jet was landing.
Police are also looking into possible professional negligence in the case, according to media reports.
Transcripts released by authorities show air traffic control ordering the Coast Guard plane to proceed to a holding point near the runway minutes before the crash, instructions the pilot appeared to have read back in acknowledgement.
Japanese authorities said on Wednesday the passenger jet received permission to land, but the smaller plane had not been cleared for take-off, based on the transcripts.
The Coast Guard pilot said after the crash that he had been given permission to enter the runway, Coast Guard officials have said.
Authorities have only just begun their investigations and aviation experts say it usually takes the failure of multiple safety guardrails for an airplane accident to happen.
A notice to pilots before the accident suggested a strip of stop lights embedded in the tarmac as an extra safety measure to prevent wrong turns was out of service, according to a copy of the bulletin posted by US regulators.
Japan Transport Safety Board (JTSB) is leading the safety investigation, and has been joined by 14 overseas investigators from Airbus, French and British authorities and a representative from the jet's engine maker Rolls Royce, a JTSB official said.
Police are also investigating, the official said.
JAL estimated on Thursday the disaster would result in an operating loss of about 15 billion yen ($A149 million).
All 379 people on board the JAL Airbus A-350 jet escaped before the plane was engulfed in flames. (AP PHOTO)
The loss of the aircraft will be covered by insurance, the company said, adding it was assessing the impact on its earnings forecast for the financial year ending March 31.
The airline was discussing compensation individually with passengers, two of whom had pets that died in the incident, JAL officials said
Insurance industry sources have said US insurer AIG was the lead insurer on a $130 million "all-risks" policy for the two-year-old plane destroyed by the fire.
AIG declined to comment.
It was the first-ever hull loss globally for the A-350 model, according to Aviation Safety Network.
The type, made largely from carbon composite, entered commercial service in 2015.
Shares of JAL fell as much as 2.4 per cent as trading resumed after the New Year's holidays, before closing up 0.8 per cent.
From the moment of the collision, it took the crew 18 minutes to get everyone off the plane and safely accounted for.
Japan's second-biggest airline has detailed how the crew in the smoke-filled cabin followed emergency procedures in textbook fashion, even as passengers panicked, intercom systems failed and several evacuation chutes were out of use due to the fire.
Most of the passengers on the flight from Hokkaido were Japanese with at least 43 foreigners confirmed among them including Australians, Swedish, Hong Kong, Chinese and South Korean nationals, a JAL spokesperson said.
A Coast Guard official on Wednesday said they had recovered a voice recorder from the Coast Guard plane.
