Eagle Air general manager Carrie Hurihanganui said in a statement the service, introduced in 2004, had always struggled commercially and was "not projected to break even in the near future".
Lake Wanaka Tourism general manager James Helmore said he had an "overwhelming feeling of disappointment", as the tourism body had worked closely with Air NZ to increase flight frequency and availability.
"I guess Air New Zealand have ultimately made a call on the viability of it," he said of Wanaka's only scheduled air service.
"It's frustrating because we had quite big plans in terms of what we wanted to do and see at the airport, so it's a setback to those aspirations."
Wanaka was heavily reliant on tourism and more work needed to be done to diversify its economic base to attract other businesses to operate in the town, improving the viability of airline services in and out of the area, he said.
Wanaka Chamber of Commerce president Leigh Stock was on hand to welcome the original Eagle Air flight eight years ago, and while he accepted the decision to cancel the service was a "sign of the times", he was extremely disappointed.
"When we welcomed the flight in 2004, we didn't expect to be saying goodbye to it in 2012. We would have expected to see more frequency, different aircraft ... but obviously as a business model it hasn't worked for Air New Zealand."
Ms Hurihanganui said the lack of profitability of the route had been exacerbated by Christchurch International Airport's decision to raise landing fees 63% from next month, with another increase planned for July.
The Queenstown Lakes District Council also raised rental costs for facilities at Wanaka Airport last year.
Queenstown Mayor Vanessa van Uden told the Otago Daily Times a "modest" rental of $19,000 was charged for Eagle Air's use of a council-owned building as a terminal.
There would be no council redundancies as a result of the service being suspended, she said.
Ms Hurihanganui said average fares for the route had gone down 4% over the past five years but for the route to break even, fares would have needed to rise 40%.
A check of airline websites yesterday showed a one-way Eagle Air fare from Wanaka to Christchurch on Friday would cost $209, while the cheapest Air NZ and Jetstar fares from Queenstown to Christchurch were $169.
Ms Hurihanganui said the airline had worked hard for eight years to try to make the route work.
"We've tried increasing schedule frequency, different service timings, reducing fares, investing in promoting the service and working with local stakeholders.
"All of this has proved unsuccessful and only added to the hundreds of thousands of dollars we have lost on this route over the years."