Air New Zealand says it will have to cancel 25 regional flights each week because air traffic control tower staff will take lunch breaks from Wednesday.
In a statement the airline called the situation farcical.
Employment Relations Act changes which come into effect on Wednesday will see the Air Line Pilots Association insisting that members take their breaks at scheduled times rather than working flexibly as they have in the past.
Air New Zealand says this means the Civil Aviation Authority from Wednesday will be forced to close five towers, twice each day, for 30-45 minutes.
Air New Zealand short haul head Bruce Parton said it was farcical that services to five regional airports would have to be cancelled.
"We have been working hard to avoid redundancies across the business where possible, and it is disappointing that this action will put jobs at risk at two of Air New Zealand's regional airlines - Air Nelson and Eagle Air," Mr Parton said.
Regional customers will face disruption and reduced frequency as Air New Zealand is forced to remove approximately 2500 seats each week from regional capacity.
Air New Zealand also stands to lose up to $3 million in revenue through the cancellation of these services to Gisborne, Napier, New Plymouth, Rotorua and Invercargill Airports.
"We appear to be the victims of an overly rigid dictate to business on how to achieve a healthy and -safe workplace, not to mention further constraints to the agility and adaptability we need in these incredibly challenging times," he said.