However, five out of the six crew of the Coast Guard aircraft are unaccounted for, while the captain escaped, a Coast Guard spokesperson said.
Footage on public broadcaster NHK showed the Japan Airlines Airbus A350 bursting into flames as it skidded down the tarmac after landing on Tuesday. It was later overwhelmed by the blaze despite feverish efforts by rescue crews to control the fire.
Miraculously, all 367 passengers and 12 crew were evacuated.
The aircraft burst into flames as it skidded down the tarmac at Tokyo's Haneda airport. (AP PHOTO)
Footage and images shared on social media showed passengers shouting inside the smoke-filled cabin and running across the tarmac away from the blaze.
The Coast Guard said the collision involved one of its planes that was headed to Niigata airport on Japan's west coast to deliver aid to those caught up in a powerful earthquake that struck on New Year's Day, killing at least 48 people.
A spokesperson at Japan Airlines said its aircraft had departed from Shin-Chitose airport on the northern island of Hokkaido.
Japanese Prime Minister Fumio Kishida instructed relevant agencies to co-ordinate to assess the damage swiftly and provide information to the public, according to his office.
Haneda has closed all runways following the incident, a spokesperson for the airport said.
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