Air New Zealand general manager domestic Scott Carr blamed the cut on a drop in demand for the service between the two cities.
"Over recent months, we’ve seen domestic demand soften in response to a tough economic backdrop. This is most evident on some of our regional network.
"Concurrently, we also have aircraft out of service due to global engine maintenance issues," Mr Carr said.
The company said it was working to re-accommodate those who had already booked to travel on the route.
"We know this change may cause inconvenience for some, but we want to assure our customers that we remain committed to connecting Invercargill to our wider network via the direct Christchurch and Auckland services."
Additional flights from Christchurch to Invercargill would be added to "ensure there is sufficient capacity".
The change will come into effect from January 19 2025.
