The Transport Accident Investigation Commission (TAIC) said it had opened an investigation.
"A search aircraft was dispatched [Saturday] night but was unable to reach the area due to weather," said TAIC's chief investigator of accidents, Captain Tim Burfoot.
"Another aircraft was dispatched to the area at first light this morning and the wreckage was located in steep terrain in the area where the aeroplane was last observed.
"The two occupants were reported to be qualified flight instructors."
Three commission investigators were expected to arrive at the site Monday morning.
The plane had left from Palmerston North and was flying to Ardmore Airport near Auckland, via Taupō Airport.
Ardmore Flying School chief executive Ian Calvert said the plane was carrying two experienced male instructors and he had been in touch with the families and friends of the men.
"It's the first fatal incident for Ardmore Flying School in a very long history of teaching pilots to fly," he said.
"It's been quite a shock to the team at work and today has been a day of supporting each other ... generally coming to terms with it.
"We're looking to support [the families] in any way that we can because how much more difficult for them it must be and we just feel for them immensely."
Calvert said they lost radio contact with the plane about 9pm last night as it was approaching Taupō.
"At this point there is no indication as to what may have occurred. They are both very experienced flight instructors."
Calvert said the area where the instructors crashed was very steep high country.
