Five Eagle Air flights from Hood Aerodrome in Masterton have been cancelled in the past two weeks but parent company Air New Zealand said it was nothing to do with passenger numbers.
Instead, the company is blaming unspecified "engineering issues" for the actions.
In an email to Eagle Air executives, Masterton Mayor Garry Daniell said passengers were becoming increasingly concerned about the reliability of the Masterton to Auckland flights.
He said he has been approached by people saying there is speculation over the company cancelling flights when bookings are light.
"The disruption to passengers involved, and to their families, is obvious," he said.
Replying to Mr Daniell, Eagle Air general manager Carrie Hurihanganui said there were five cancellations due to "engineering issues" over a two week period.
The company operates 18 aircraft making just under 160 flights a day throughout New Zealand so several sectors are affected when a flight is cancelled.
"Decisions to cancel flights are not something we take lightly, as we are acutely aware of the disruption it causes our customers," she said.
Eagle Airways does not have a policy of cancelling flights when bookings are light, according to Ms Hurihanganui.
She apologised to those affected by recent flight cancellations and said to contact her directly if they have any further questions or feedback.
When asked by Wairarapa Times-Age to explain the "engineering issues", Air New Zealand spokeswoman Tracy Mills would only confirm the flights were cancelled, without giving details of the issues involved.
"I can confirm that unfortunately five Eagle Air flights were cancelled due to engineering requirements," she said.
Masterton District Council contributed $870,000 to the airport upgrade project so that from 2009, Eagle Air could run Monday to Friday flights to and from Auckland, and a Sunday evening flight from Auckland to Masterton.