Five people who were on board the coastguard plane have died, AFP news agency quotes Japan’s transport minister as saying.
State broadcaster NHK has also reported five dead. The captain escaped but is severely injured, it adds.
It’s believed the coastguard aircraft, which was taking food to areas hit by Monday’s powerful earthquake, collided with the Japan Airlines plane as it landed on the runway.
Posting on X, his office says he wants to ensure that officials “quickly ascertain the damage situation”.
He also wants to “strive to provide appropriate information to the public”.
Josh Coultas who was in Tokyo Haneda Airport has described his emotions as news filtered through the terminal about the Japan Airlines fire on the runway.
He tells the BBC it was scary “watching the airport freeze”.
Josh says as he was at the airport waiting for a friend coming in on a different flight.
“It was shocking because my friend could have been on that plane – but they weren’t,” he adds.
“All flights are cancelled – I don’t think they’ll come back today.
“With the earthquake and tsunami and now this it has been quite a scary start to 2024 in Japan.”
Prof Graham Braithwaite, director of transport systems at Cranfield University in the UK, has praised efforts made by the cabin crew and pilots onboard the Japanese Airlines (JAL) flight.
“Japan has a phenomenal record when it comes to transport safety,” Prof Braithwaite tells the BBC as he describes JAL as a “world leader” in safety.
“The evacuation has been successful and it is a reminder how much has gone into training cabin crew.
“Their focus is on safety. They are the last people to evacuate the airplane and on face value, it looks like they have done an incredible job.”