The accident was a national disaster and remained the worst aviation accident on New Zealand soil, the Rev Waugh said.
Family and friends of those who perished wiped away tears as a solemn roll call of the 23 killed was read out.
Flowers and wreaths were laid on the memorial before a fly-over by a historic DC-3 aircraft, nearly identical to the one that crashed 50 years ago.
The Rev Waugh also read a statement on behalf of pioneer helicopter pilot Mike Alexander, who loaded his little petrol-powered Hiller 12E helicopter on to a trailer and drove it through the night from Wanganui to help with the crash recovery in 1963.
Mr Alexander said in his statement that the impact of finding the crash had never left him.
"For all those years and during my own flying, it served as a reminder on a number of occasions. Sadly, cold hands can't receive the flowers, but they never fade."
Matamata-Piako Mayor Hugh Vercoe said the crash was a part of the region's history which needed to be remembered.
Guild of Air Pilots and Air Navigators Wing Commander Gordon Ragg said the crash had led to major changes in aircraft safety practices, including weather briefings along air routes, the carriage of crash-proof radio beacons, and investigations into the fitting of flight recorders.
Air New Zealand chief flight operations and safety officer Captain David Morgan said it was important to always remember those who had been lost in the tragedy.
"Some of you will be floating on a sea of grief, coming here to remember those who were close to you and you have lost.
"We share that sense of loss, but hopefully that sea of grief will be a little calmer now, knowing that the industry and aviation has learned from tragedies such as this."
Some of the rescuers involved in the search, including David Gould, 74, spent the night at the crash site to commemorate the tragedy.
Also at the commemoration was Errol Board who, aged 32, was working at the nearby Te Puna Quarry at the time. "I was just going across to the smoko room and I heard this plane coming.
"I just listened intently because there was no way that a passenger plane [was meant to be] there. It was way off track."
The ceremony was a fitting tribute, Mr Board said.