All 379 passengers and 12 crew on board the passenger plane which burst into flames were safely evacuated, Japanese transport minister Tetsuo Saito told reporters.
But five of the six crew members from the smaller plane — bound for central Japan after Monday's huge earthquake — died, Saito said.
The captain escaped and survived but was injured, he said, cautioning that "we're not at the stage to explain the cause" of the accident.
Television and unverified footage shared on social media showed the Japan Airlines (JAL) airliner moving along the runway before a large eruption of orange flames and black smoke burst from beneath and behind it.
Video posted to social media platform X showed people sliding down an inflatable emergency slide from the side of the passenger plane while flames shot out from the rear of the aircraft.
All 367 passengers plus 12 crew onboard were swiftly taken off the plane before dozens of fire engines with flashing blue lights sprayed the fuselage.
They however failed to put out the flames coming out of windows near the wings and the blaze soon engulfed the entire aircraft.
The plane, reportedly an Airbus 350, had arrived from New Chitose Airport serving Sapporo on the northern island of Hokkaido. Those on board included eight children.
In this image made from video, a Japan Airlines plane is on fire on the runway of Haneda airport on Tuesday, January 2, 2024 in Tokyo, Japan. Courtesy NTV via AP.
"Smoke began to fill the plane, and I thought, 'this could be really bad'," an adult male passenger told reporters at the airport.
"An announcement said doors in the back and middle could not be opened. So everyone disembarked from the front," he said.
A female passenger said it had been dark on board as the fire intensified after landing.
"It was getting hot inside the plane, and I thought, to be honest, I would not survive," she said in comments shown on broadcaster NHK.
'Earthquake mission'
The coast guard plane had been preparing to fly to Ishikawa prefecture to deliver supplies after the devastating New Year's Day earthquake which killed at least 48 people.
Prime Minister Fumio Kishida praised the deceased crew members on their way to help the victims of the quake.
"These were employees who had a high sense of mission and responsibility for the affected areas. It's very regrettable," he told reporters. "I express my respect and gratitude to their sense of mission."
JAL said the passenger plane either collided with the other aircraft on a runway or a taxiway after it touched down, Kyodo reported.
There was also burning debris on the runway at Haneda, one of the world's busiest airports.
Haneda suspended domestic flights, according to its website, but most international takeoffs and landings were still operating.
A transport ministry official said investigations into the incident were ongoing, including exchanges between the flights and air traffic control.
Japan has not suffered a serious commercial aviation accident in decades.
Its worst ever was in 1985, when a JAL jumbo jet flying from Tokyo to Osaka crashed in central Gunma region, killing 520 passengers and crew.
That disaster was one of the world's deadliest plane crashes involving a single flight.