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The plane's wreckage was found this morning in steep terrain after being reported missing last night.
The bodies of two men have now been recovered, police said in a statement.
Earlier, the Transport Accident Investigation Commission (TAIC) said it had opened an investigation into what it calls an "aviation accident" in the Kaimanawa Ranges in the Central North Island.
The Diamond DA42 Twin Star aeroplane was last seen on radar about 22 nautical miles south-southeast of Taupo. It was reported missing last night about 10pm.
A search team found the small plane, which was carrying two experienced flying instructors, this morning.
"A search aircraft was dispatched last 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 ."
The Commission has appointed a team of three investigators. They are expected to arrive at the site tomorrow morning.
The Herald has sought an update from police who said more information will be released as it comes to hand.
A Maritime New Zealand spokeswoman confirmed the search teams had found the plane this morning. The response was now being led by police.
Police confirmed the plane was located at 11.30am today. Poor weather last night and earlier today had prevented a helicopter search.
A major search operation had been under way for the missing plane, a DA 42 twin-engine propeller aircraft registered to Ardmore Flying School in Auckland.
A Rescue Coordination Centre spokeswoman told the Herald it was alerted about 10.30pm on Saturday and police were notified about 11.50pm.
The plane had left from Palmerston North and was flying to Ardmore Airport near Auckland, via Taupō Airport.
Ardmore Flying School CEO Ian Calvert said the plane was carrying two experienced male instructors. He had been in touch with the families and friends of the men.
"It is just awful. We are all just waiting for the rescuers to let us know what has happened, hoping and praying for a safe outcome."
Calvert said they lost radio contact with the plane at about 9pm 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.
A rescue helicopter was mobilised last night and tried to reach the last-known location of the plane, 24km east of Tūrangi, but had to turn back because of low cloud and drizzle.
There was more low cloud and drizzle this morning and the rescue team was waiting for conditions to improve earlier before they could get in the air.
The alarm was first raised by Airways - which looks after air traffic control - at 10.30pm on Saturday.