The Airbus A350 jet collided with a Coast Guard aircraft on the runway.
All passengers were safely evacuated from the airliner, but five out of six personnel on the smaller Coast Guard plane were killed.
Officials say the flight data recorder from the Airbus has been recovered.
But the cockpit voice recorder has not yet been found.
The wreckage should now be removed by Sunday (January 7), and will then be inspected by Tokyo police.
Transport authorities want to establish why the Coast Guard plane entered the runway as the airliner was landing.
Local media reports say police are looking into possible professional negligence.
The captain of the Coast Guard plane - the sole survivor - is under close scrutiny.
Transcripts from the airport's control tower appear to show that he was told to stop short of the runway before the crash occurred.
Haneda is the world's third-busiest airport, and authorities say it was at full capacity at the time of the incident.
Reuters has reported that the Coast Guard plane was flying its third mission within 24 hours.
It had been flying people and supplies to support recovery efforts in the region of Japan's recent earthquake.
Now experts say multiple safety procedures must have failed for the accident to occur.
They will also be looking closely at the catastrophic fire suffered by the Airbus plane.
It's the first such blaze on one of the new generation of jets, which are largely made of carbon-composite materials instead of metal.
Aviation safety experts say the fact that the plane held together long enough to get everyone off should renew confidence in the materials.
