Footage shared on X, formerly known as Twitter, shows the A350-900 skidding along the runway in flames when it touched down at Haneda.
National and international news agencies report the aircraft, flight JAL516, collided with a coastguard aircraft upon landing.
Japanese broadcaster HNK said all 379 passengers and crew onboard the aircraft were safely evacuated. The AFP news agency, meanwhile, said five of the six people onboard the coastguard aircraft have been killed. The captain is understood to have survived suffering severe injuries.
It is reported the flight had taken off from Hokkaido, the northernmost of Japan’s main islands more than 1,200km away from Tokyo.
The crash landing came just a day after nearly 50 people were killed following a powerful earthquake that struck the country’s Noto peninsula and surrounding areas of central Japan on New Year’s Day (1 January).
The magnitude-7.6 quake caused extensive structural damage and fires in the city of Wajima in Ishikawa Prefecture.
The full extent of damage is still being determined, as rubble and severed roads are hampering rescue operations, Kyodo News Agency reported.
Further aftershocks remain a possibility and some transport links are disrupted, the Foreign Office said.
It added: “If you are in the affected areas, please follow the instructions from the local authorities and check the latest information on NHK World News.”
Tsunami warnings covering extensive areas along the Sea of Japan were lifted on Tuesday morning.
The highest wave of at least 1.2 metres reached Wajima Port on Monday following the 4.10pm quake.
