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.
Insurance industry sources have said U.S. insurer AIG (AIG.N) was the lead insurer on a $130 million "all-risks" policy for the two-year-old JAL Airbus (AIR.PA) A350 widebody jet that was destroyed by a fire after the collision at Tokyo's Haneda airport.
It was the first-ever hull loss globally for the A350 model, according to Aviation Safety Network. The type, made largely from carbon composite, entered commercial service in 2015.
Shares of JAL rose 0.5%, showing a muted reaction to the crash as trading resumed after the New Year's holiday. They initially fell as much as 2.4% before recovering from that drop.
All 379 people aboard the JAL airliner managed to evacuate the burning plane after the collision. Five of six crew on the Coast Guard aircraft were killed in the crash.
Japanese authorities said on Wednesday the passenger jet had been given permission to land, but the smaller plane had not been cleared for take-off, based on control tower transcripts.
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 airplane accident to happen.
Separately, nearly 200 passengers were stranded overnight at New Chitose airport near the northern Japanese city of Sapporo, from which flight JL516 had departed, as flights arrived late due to delays, a spokesperson for airport operator Hokkaido Airports said on Thursday.
($1 = 143.1100 yen)
