Images shown by NHK showed the jet going down the runway before a massive burst of orange flames erupted beneath and behind it.
According to NHK, all 367 passengers and 12 staff members on the Airbus airliner were evacuated. According to Kyodo News, there were eight children on board.
According to NHK, one of the six crew members aboard the Coast Guard plane was safe, while the other five were not.
The reason for the incident was not immediately obvious, although according to television sources, the Airbus crashed into a Coast Guard aircraft.
According to the Jiji news agency, the coast guard jet was due to travel to assist with rescue efforts following a big earthquake in central Japan on Monday.
According to reports, the aircraft had just landed at Sapporo Airport on the northern Japanese island of Hokkaido.
A Coast Guard spokesman said they were "checking details" at Haneda Airport, one of the busiest in the world.
"It's unclear whether there was a collision. "But our jet is definitely engaged," he told AFP.
According to Kyodo, JAL stated that the passenger plane crashed with the second aircraft after touching down on a runway or a taxiway.
Footage taken by a passenger inside the plane appears to show flames shooting from beneath the plane before the cabin fills with smoke. The clip could not be verified by AFP.
According to Kyodo, the Ministry of Land, Infrastructure, Transport, and Tourism is investigating the incident.
The television footage showed flames shooting out of the windows as rescue personnel doused the jet before the flames devoured the entire airliner.
There was also flaming debris on the runway, and the airport was closed to traffic, according to reports.
According to NHK, more than 70 fire engines were mobilized.
Japan hasn't had a major commercial aviation disaster in decades.
The deadliest incident occurred in 1985, when a JAL jumbo aircraft flying from Tokyo to Osaka crashed in the central Gunma area, killing 520 passengers and crew.
That accident was one of the world's deadliest single-flight jet disasters.