Live footage on public broadcaster NHK showed the aircraft erupt 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 spokesperson at Japan Airlines said the aircraft had departed from Shin-Chitose airport on the northern island of Hokkaido.
Haneda has closed all runways following the incident, a spokesperson for the airport said.
(Inputs from Reuters)
