The plane was identified by a Japan Airlines spokesperson as flight 516, traveling from Shin-Chitose airport in Hokkaido to Haneda, according to Reuters.
Haneda is one of Japan's busiest airports.
Japan Airlines said all 379 people on board the burning aircraft, both passengers and crew members, were evacuated.
Video footage broadcast live on public broadcaster NHK showed fire crews working to put out the blaze.
The Japanese Coast Guard said it was investigating the cause of the incident, suggesting the possibility that one of its own aircrafts collided with the passenger jet.
"It's not clear if there was a collision. But it is certain that our plane is involved," a Coast Guard official told the French AFP news agency.
Meanwhile, Japan's broadcaster NHK reported that five people who were onboard the Japan Coast Guard plane which likely collided with the passenger jet were unaccounted for.
MNA/PR
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