However, the changes would not affect jobs, and the airline would restore the flights if the demand grew.
Mayoral candidate John Morrison said the news was a "body blow" to Wellington's already sluggish economy.
"How can we rebuild the Wellington economy when the national airline carrier doesn't have confidence in the nation's capital? What message does that send out to businesses, tourists and overseas students?"
The reductions would also compromise the airport's plans to extend its runway to secure more long-haul flights.
"We need to step up the pace, otherwise we're in danger of becoming a backwater. We're talking about extending the runway and here we are, our very own national carrier is reducing services," Mr Morrison said.
"It is another example of an Auckland vortex dragging everything it can from the rest of NZ and it seemed Air NZ wanted to intensify the Auckland and Christchurch hubs at Wellington's expense."
News of the cuts had been kept under wraps thanks to the approaching elections, which Mr Morrison said was "scandalous".