NHK TV reported that all occupants of Japan Airlines flight JAL-516, believed to total 379 people, got out safely before the plane was entirely engulfed in flames. The Japanese coast guard said the pilot of its plane had escaped.
NHK reported that the five other crew members had been found dead.
Local TV video showed a large eruption of fire and smoke from the side of the Japan Airlines plane as it taxied on a runway.
The area around the wing then caught fire. Footage an hour later showed the plane fully on fire.
NHK TV said the plane was an Airbus A-350 that had flown from Shin Chitose airport, near the city of Sapporo, to Haneda.
Coast Guard spokesperson Yoshinori Yanagishima confirmed the collision between the passenger plane and its flight MA-722, a Bombardier Dash-8.
Swede Anton Deibe, 17, who was a passenger on the Japan Airlines plane, told Swedish newspaper Aftonbladet that "the entire cabin was filled with smoke within a few minutes.
"We threw ourselves down on the floor," he said.
"Then the emergency doors were opened and we threw ourselves at them."
Deibe was travelling with his parents and sister.
"The smoke in the cabin stung like hell. It was a hell," he said.
"We have no idea where we are going so we just run out into the field. It was chaos."
Kyodo said the coast guard plane, which is based at Haneda, had been due to head to Niigata to deliver relief goods to residents affected by a deadly earthquake in the region on Monday that killed at least 48 people.
Haneda is one of the busiest airports in Japan, and many people travel over the New Year holidays.
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