Audio By Carbonatix
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."
Latest Stories
-
US seizes second oil tanker off Venezuela’s coast
8 minutes -
Australian PM announces intelligence review as country mourns Bondi attack
18 minutes -
Imran Khan and wife given further jail terms after state gift fraud case
19 minutes -
5 perish in fatal collision on Cape Coast–Takoradi Highway
31 minutes -
Poultry imports driving egg glut – GAPFA
1 hour -
Legal lifeline for Ghanaians in America as lawyers association, Embassy move to tackle diaspora challenges
2 hours -
Photos: First Atlantic Bank PLC officially listed on Ghana Stock Exchange
2 hours -
Energy minister assures stable power as Ghana hits peak demand in December
3 hours -
Miguel Ribeiro Fiifi Brandful
3 hours -
Adom TV’s ‘Nine Lessons and Carols’ electrifies National Theatre in a festive extravaganza
3 hours -
Mahama orders $78m payment to Justmoh to resume Agona–Nkwanta road works
3 hours -
Christmas rush deepens traffic woes in Accra Central
4 hours -
Three arrested after viral video shows toddler being fed alcohol
4 hours -
Survivors ‘nervous and sceptical’ about release of remaining Epstein files
5 hours -
‘No room for egos’: Sam Jonah issues bold challenge to UCC graduates and Ghana’s future leaders
5 hours
