Yamashita says that he notes the fact that the collision took place on a runway.
The transport ministry's Civil Aviation Bureau says the accident occurred on runway C of the airport.
It is a normal operation to use the same runway for both landings and take-offs.
But if there is an aircraft about to land, planes waiting to take off stay on the taxiway. They won't be allowed to enter the runway.
The opposite is the same. If there is an aircraft trying to take off, an approaching aircraft won't land on the same runway.
So, the question remains as to why the two planes were on the same runway.
Discrepancies among the three parties
Yamashita says details of instructions from air traffic controllers, as well as how pilots of both of the planes perceived their instructions, will be the focus of the investigation to determine the cause.
The transport ministry released on Wednesday the transcript of communication between air traffic control and two aircraft.
It shows that at 5:43 p.m., or four minutes before the collision, air traffic control instructed the JAL aircraft to continue its approach to the runway for landing. Air traffic control also informed the aircraft at the time that there would be a departing plane by saying "We have a departure."
Two minutes later, air traffic control cleared the JAL jet to land on the runway by saying "JAL 516 Runway 34R cleared to land, wind 310/8."
JAL had already stated that the flight crew said they received and repeated the control tower's permission to land before the final descent.
At 5:45, the tower instructed the Coast Guard aircraft to stay short of the runway, by saying "JA722A Tokyo Tower. Good evening. No.1, taxi to holding point C5."
JA 722A is the Japan Coast Guard aircraft.
The transcript shows the Coast Guard pilot repeated it as "Taxi to holding point C5, JA722A No.1. Thank you."
As far as is shown in the transcript, air traffic control did not permit the coast guard plane to enter the runway from this communication up until the collision.
But a source from the Coast Guard said the surviving pilot told them, "We entered the runway as we received permission to do so."
The Japan Transport Safety Board began a full-scale investigation on Wednesday. Officials have already recovered the black box of the Japan Coast Guard plane. They plan to interview the captains of both planes.