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 on Tuesday.
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.
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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.