Dramatic video footage shows the moment the plane erupted into a ball of flames at about 5:55 p.m. local time.
Japan Airlines flight 516 took off from New Chitose Airport in Hokkaido to Tokyo’s Haneda Airport, according to NHK.
The crash comes just a day after a massive earthquake ripped through Ishakawa, Japan.
It is believed the Airbus A350, which can carry up to 480 paasengers, collided with a Japan Coastguard aircraft as it landed.
Only one person has been accounted for from the coastguard aircraft that was carrying aid to parts of the country hit by yesterday's earthquake.
Firefighters are tackling the blaze and it is believed all 400 passengers have been evacuated from the passenger jet.
Aviation sources said A plane burst into flames on the runway of Tokyo's Haneda airport on Tuesday, with news reports saying it hit another aircraft after landing.
NHK TV reported that all passengers aboard, believed to have been about 400 people, got out safely
Local TV video showed a large eruption of fire and smoke from the side of the Japan Airlines plane as it taxied on a runway. The area around the wing then caught fire.
It said the plane was JAL flight 516 had flown out of Shin Chitose airport in Japan to Haneda.
Later, video showed fire crews working to put out the fire with streams of water. The flames had spread to much of the plane.
NHK quoted JAL as saying it believed its plane was hit by another aircraft, possibly a Japan Coast Guard plane.
Japan's Coast Guard said it is checking reports about a collision between its aircraft and the JAL flight on fire. It had no further details
Haneda is one of the busiest airports in Japan, and many people travel over the New Year holidays.
