Eyewitness footage captured passengers running across the tarmac after leaving the Airbus A350 aircraft on an evacuation slide, having landed from the northern island of Hokkaido.
Five of the six crew in the other smaller aircraft died, according to Japan's transport minister:
"Japan Airlines informed Japan's Civil Aviation Bureau that 379 people including 367 passengers and 12 crew members had been safely evacuated. Regarding the Coast Guard plane, one captain was evacuated but 5 other crew members were confirmed dead."
The Japan Airlines plane was overwhelmed by the blaze despite efforts by rescue crews to control it.
Broadcaster NHK, citing the Tokyo Fire Department, said at least 17 people on board were injured.
The Coast Guard said the collision involved one of its planes headed to Niigata airport on Japan's west coast to deliver aid following the powerful earthquake which struck on New Year's Day, killing tens of people.
Japanese Prime Minister Fumio Kishida's office said he had called for a swift assessment of the damage.
A Haneda airport spokesperson confirmed all runways were closed and flights cancelled following the incident.
