Japan Airlines (JAL) revealed on Thursday an expected loss exceeding $100 million after one of its planes was destroyed in a collision with another aircraft on the runway at Tokyo's Haneda airport this week.

Despite the Airbus A350 widebody jet being completely engulfed in flames that took over six hours to extinguish, all 379 people on board managed to escape unharmed.

However, the smaller Coast Guard plane, on its third mission to deliver aid to quake-hit regions on Japan's west coast, tragically lost five of its six crew members, with the surviving pilot sustaining severe injuries.

Transport authorities are currently investigating the circumstances that led to the Coast Guard plane entering the runway where the passenger jet was landing. Media reports suggest police are also looking into potential professional negligence in the case.

Transcripts released by authorities indicate that air traffic control instructed the Coast Guard plane to proceed to a holding point near the runway just moments before the crash, instructions the pilot seemingly acknowledged.

Japanese authorities stated that the passenger jet had been given permission to land, while the smaller plane had not been cleared for takeoff, according to the transcripts.

The ongoing investigation involves the Japan Transport Safety Board (JTSB) leading the safety inquiry, with collaboration from 14 overseas investigators from Airbus, French and British authorities, and a representative from the jet's engine maker, Rolls Royce. In parallel, the police are conducting their own investigation.

JAL estimates an operating loss of approximately 15 billion yen ($105 million) due to the disaster. While the loss of the aircraft is expected to be covered by insurance, the impact on earnings forecasts for the financial year ending March 31 is still being assessed.

The airline is engaging in individual compensation discussions with passengers, including those who lost pets in the incident.

The tragic collision, resulting in the first-ever hull loss globally for the A350 model, has caused disruptions at Haneda airport, impacting hundreds of flights and leaving frustrated passengers dealing with cancellations and delays. JAL's shares fell initially but recovered slightly after the New Year's holidays, closing up 0.8%.