Television footage showed the plane touching down at about 6.50 am local time.
The rear wheels hit the tarmac and then the aircraft's nose hit the runway before the plane bounced onto its left wing, exploding into flames and skidding at high speed while billowing black smoke.
The plane then flipped onto its left side and came to a halt off the side of the runway.
According to the Japan Meteorological Agency, unusually strong winds of around 76km per hour were blowing through the city of Narita on Monday morning around the time of the crash.
|Strong winds were blowing through the area at the time of the crash [AFP]
Meteorological officials at the airport said they had warned airlines of a risk of wind shear – a sudden and localised change in wind speed or direction that can destabilise an aircraft.
The aircraft crashed on Narita's longest runway, disrupting dozens of flights at the busy airport.
Ikuo Uda, a spokesman for Narita International Airport Corporation, which manages the airport, told the Associated Press that 16 international flights were cancelled, and that the airport was operating with only one runway several hours after the crash.
Narita airport is a major international hub located about 60km east of central Tokyo.
It is Japan's second-busiest airport, after Haneda Airport, a largely domestic hub in the capital.
Strong winds and turbulence have caused other recent incidents at the airport.
Last month, a flight from the Philippines was affected by severe turbulence as it circled prior to landing, injuring 50 passengers and crew members.