Five out of six people on the smaller coastguard aircraft died.
Passengers on the Japan Airlines Airbus A350 flight 516 were evacuated by inflatable slides as the cabin filled with smoke.
Everyone on passenger jet manages to survive
One UK travel expert said the flight crew had done "an incredible job" to get everyone off safely.
The coastguard De Havilland Dash was preparing to fly from Haneda Airport in Tokyo to Niigata to deliver relief after the earthquake near there on Monday.
Video from inside the passenger plane showed smoke billowing in.
In different footage, terrified passengers escaped down an inflatable slide.
Swedish passenger Anton Deibe, 17, said: "The smoke stung like hell. It was hell."
Another passenger said of the collision: "I felt a boom like we had hit something and jerked upward the moment we landed.
"I saw sparks outside the window and the cabin filled with gas and smoke."
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