A discussion on the new OneUp system at the Flyertalk forum attracted hundreds of responses within days.
Many of those who commented opposed the system, calling it a regressive step that alienated the airline's best customers.
User Xiaotung said OneUp was Air New Zealand frequent flyers' "worst nightmare".
"Exit strategy anyone? We have repeatedly stated that the only value of Airpoints is upgrades. Now they have taken the one and only good thing about Airpoints away.
"Time to say good bye to NZ."
Air New Zealand partially backed down on the OneUp changes in the face of the criticism.
It announced top "Gold Elite" status supporters would be exempt from the system - on the condition they did not upgrade by more than one seat class.
In a statement the airline also said changes were made following a successful trial. It said the programme gives all passengers the opportunity to upgrade on international flights where there are premium cabins.
Despite that, entrepreneur Ben Kepes said Australian airline Qantas could capitalise on the discontent created by the changes to spark an exodus of Air New Zealand frequent flyers.
The self-described "Air New Zealand evangelist" said the way the OneUp system had been implemented diminished his view of the carrier.
"It's definitely left a bad taste in my mouth.
"It's a bad look when people are starting to say 'what are my options with other airlines?'...I would be surprised if there wasn't a mass exodus from Air New Zealand."
Mr Kepes said the bidding system would add unnecessary stress to frequent flyers' seat upgrade applications.
He claimed the changes compromised Air New Zealand's reputation for great service to high value customers.
"As a valuable customer you want to know you've been treated with respect. That's the problem with this. People don't feel they've been treated with respect."
Customers also had problems with how the new system was communicated to them, Mr Kepes said.
"They've tried to obfuscate the change using some kind of smoke and mirrors campaign. People don't react to that well. Especially the high value customers."