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The pilot, who has not been named, was flying over Lake Ellesmere, south of Christchurch, in a Cessna 172 owned by the Canterbury Aero Club when the plane crashed on Thursday night.
Civil Aviation Authority spokesman Mike Richards said the pilot was conducting night flying exercises.
"The aircraft suffered a high-impact landing on the mud flats of Lake Ellesmere," he said.
"The CAA has sent two safety investigators from Wellington and one from Christchurch to the crash site.
"CAA will undertake a preliminary visual assessment of the site this morning using an authorised drone operator to take detailed photographs, prior to the recovery of the aircraft.
"Any disturbance of the mudflats around the aircraft could compromise valuable evidence, so it is critical to record everything possible before moving the wreckage."
Maritime New Zealand's Rescue Co-ordination Centre picked up an emergency locator transmission about 10.20pm.
It dispatched the Christchurch rescue helicopter and ground searchers found the crash site about an hour later.
Police said the sole occupant of the plane was found deceased.
The pilot was undertaking a flight required for a night flying rating.
Canterbury Aero Club chief executive Jeremy Ford told Stuff : "It is with great regret that we must report the crash of one of our aircraft on a routine training flight over Lake Ellesmere.
"The pilot has not survived the impact."
Mr Ford said the pilot was a member of the club.
"The club is undertaking its emergency response procedure, which will include notifying next of kin. There is no immediate indication of the cause of the crash."
Police said the death will be referred to the Coroner.
The club is based at Christchurch Airport and is New Zealand's largest aero club. It provides a wide variety of training from introductory flights to commercial licences.