The smaller aeroplane collided with a Japan Airlines (JAL) passenger jet on the runway on Tuesday.
Newly released transcripts of air traffic control instructions just before the crash confirmed the JAL Airbus A350 was cleared to land.
Permission for take-off was not given to the coastguard Bombardier Dash-8.
According to officials, the JAL flight was cleared to land on runway 34R at Haneda while the coastguard aircraft was told to "taxi to holding point C5" - a place on the airfield's taxiway system where aircraft await permission to enter the active runway for take-off.
The transcript shows the coastguard aircraft acknowledged the call from air traffic to taxi to the holding point - its last transmission before the collision.
The transcripts appear to contradict the coastguard plane's captain - the only one of the six crew to survive - who told investigators he had been given permission to enter the runway which the JAL airliner was approaching.
-- Courtesy of BBC News