
Live footage on public broadcaster NHK showed the aircraft erupting in flames as it skidded down the tarmac despite feverish efforts by rescue crews to control the blaze.
The Coast Guard said it was investigating the possibility that one of its aircraft collided with the passenger jet.
Five out of the six crew of the coast guard aircraft are unaccounted for, while one escaped, public broadcaster NHK reported.
A spokesman at Japan Airlines said the aircraft had earlier departed from Shin-Chitose airport on the northern island of Hokkaido.
Haneda has closed all runways following the incident, a spokesman for the airport said.