Japan Airlines says the airplane is Flight 516 from New Chitose Airport in Hokkaido to Tokyo's Haneda Airport, reported NHK.
Video footage showed the passenger jet moving and then igniting with a large fireball.
According to reports, people were evacuated from the flight using emergency slides.
Japan Airlines says the plane collided with what appears to be a Japan Coast Guard aircraft after landing at Haneda Airport, NHK reported.
As per flight tracking site FlightAware the aeroplane was an Airbus A350-900.
Aviation mishap in Japan
Japan has not recorded a major commercial aviation accident in decades.
In 1985, at least 520 passengers died when a JAL jumbo jet flying from Tokyo to Osaka crashed in central Gunma region.