"Due to a commercial decision, we have had to pull services out of the Far North," Manabus chief executive Sheryll Otway said.
As well as runs north of Paihia, the first morning service out of Whangarei to Auckland and the last in the evening have been axed.
There would still be three daily services connecting from Auckland to Whangarei/Whangarei to Auckland, and two a day from Paihia to Auckland, and return, Ms Otway said.
All booked and paid tickets for the withdrawn services are fully refundable, including the booking fee.
Operations manager Greg Evans said the service was one of a number of routes the company put on hold for winter.
"The only way we can make that [Whangarei to Auckland] service work is by putting a night bus up from Auckland to the Far North, which is poorly used. While I'm very sorry there are customers who have been inconvenienced, we just weren't making any money on it. We will revisit back to next summer," he said.
Flying may not be a reliable alternative. Northland tourism advocate Jeroen Jongejans has complained to Air New Zealand after passengers booked on an Auckland to Whangarei flight instead endured a three-hour unconditioned bus trip.
"When you make the investment to fly, you want to fly. I talk to business people who go to Auckland a lot - we do seem to be the poor cousin in regards to flights," Mr Jongejans said.
"As I'm sitting here talking to you, the flight from Whangarei to Auckland has been cancelled.
"We do need to improve the service because too often I talk to people who are quite disgruntled."
Tony Collins, Northland Chamber of Commerce chief executive, had heard of three Auckland/Whangarei flights being cancelled in the past two weeks.
"If that's the case that is a problem, but I don't have the numbers. I heard anecdotally it was the first and last flights being cancelled. I don't know if it's public perception that the flights are cancelled often, or if it is a regular occurrence."
Mr Collins said there could be long-term consequences to flight cancellations.
"If flights are cancelled people might say they're not going to take the risk and they're not going to use flights - and if people don't use flights will there be less available?
"For business, health and education we need a reliable public transport system."
Mr Collins said flight cancellations could have a huge impact for business people who were using the service as a connecting flight.
"If you've got a meeting in Rotorua and you've organised a flight from Whangarei to Auckland to catch your flight to Rotorua, and your connecting flight to Auckland is cancelled, that is a two-hour drive to Auckland - you've missed your meeting," he said.
An Air NZ representative said flights were occasionally cancelled at any airport due to a variety of reasons, including mechanical or weather.
"These things happen from time to time," she said.
