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
-
Kumasi to host Joy Prime’s Big Chef Tertiary S2 finals
4 mins -
KOD hints at releasing an album before he turns 50
9 mins -
2024 Election: NDC accuses NPP of printing fake ballot papers
17 mins -
A democracy that fails to solve its own problems is a questionable democracy – Dr Muhammad Suleiman
20 mins -
Our fight against corruption is more talk, less action – Mary Addah
28 mins -
CHRAJ report settles matters against Kusi Boateng – Lawyer
34 mins -
Growing dissatisfaction with democracy demands citizen-centered governance – Mavis Zupork Dome
37 mins -
Ghana’s Democracy: Choices, not elections will drive change – Benjamin Offei-Addo
42 mins -
PRESEC-Legon marks 86 years with launch of groundbreaking AI lab on November 30
45 mins -
Limited citizen participation threatens Ghana’s democracy – Prof. Kwesi Aning
55 mins -
Contractor storms basic school to drive out students from classroom, claiming government owes him
1 hour -
The quest for peaceful election: religious and traditional leaders should be part of election observers
1 hour -
NDC has better policies to boost economy through agricultural, oil sectors – Ato Forson
1 hour -
Yaw Ampofo Ankrah calls for Kurt Okraku and Executive Council to resign over AFCON failure
2 hours -
Coalition of teachers to boycott December election over unpaid salary arrears
2 hours