Otago pilots are "startled" by changes to the Civil Aviation Authority fees structure which will result in some fees rising by more than 300% over the next three years.
Transport Minister Gerry Brownlee said the new funding framework would enable the organisation to improve air safety and ensure users met the true cost of the services they received.
"Confidence in the safety and security of the civil aviation system underpins the substantial economic contribution of the aviation sector in New Zealand," Mr Brownlee said.
The changes will come into effect on November 1, when a private, recreational, commercial or airline transport pilot's licence will rise from about $56.22 to $230, and a flight instructor's licence from $51.11 to about $197.
Health checks will be standardised with a medical certificate application costing $313, and the hourly charges for surveillance and certification functions will progressively increase from $135.70 to $284 over the next three years.
Otago Aero Club president Warwick Sims said few in the aviation industry would be happy with the decision.
"It's a startling announcement.
"You wonder how there could be justification in making such a price hike when the rise in the cost of living is so much less."
Mr Sims said the increases should be spread over a longer period.
Queenstown Milford Users Group member and Air Milford chief executive officer Hank Sproull understood the reasons for the fee increases, but was frustrated because they were so steep.
"It pushes our costs up further, which we have to pass on to the customer down the line.
"Airline audits used to cost about $135 per hour. Now they're going up to $284 per hour. It could push our operations costs up by over $4000 a year."
Mainland Air chief flying instructor John Penno said the CAA had forced the increases on to the aviation industry and he was angry it was powerless to do anything about it.
"We can complain, but nothing will happen.
"What I would like to know is, how come they allowed the situation to develop to the point where they have to increase the prices by 300%? It's just crazy."
An Office of the Auditor-General's review in 2010 said the CAA was falling behind modern practice and having difficulty keeping pace with growing sector demand and complexity.
Mr Brownlee said the funding framework had not been reviewed for more than 15 years. The recent review would ensure the CAA had sufficient revenue to fund operations and improve services.
The new fees were expected to deliver $14.1 million in the next three years.
He said the overall impact on aircraft operators was expected to be relatively small.
