An Air New Zealand flight from Auckland to Christchurch was delayed after a firearm was found in the hold of the aircraft by security teams.
Flight NZ547 had been due to depart at 2pm when the pilot announced that passengers had tried to bring a rifle on to the plane, but failed to follow correct check-in procedure, a passenger on the plane said.
However, the Civil Aviation Authority said the firearm was being transported lawfully.
"Security procedures identified a firearm in a bag in the hold of an aircraft on a flight bound for Christchurch," it said in a statement.
"Precautionary checks were carried out and determined that the firearm was being lawfully transported."
It said the firearm was not in the plane's cabin and presented no risk to passengers.
It said that while Aviation Security regretted the inconvenience to passengers, public safety was its number one priority
An Air NZ spokeswoman said the flight had been delayed when Aviation Security requested a passenger's checked bag be taken out of the airliner's baggage hold.
"At no time did anyone attempt to board the flight carrying a firearm," she said.
"The passenger who owns the bag had already boarded and was completely compliant when asked to disembark. They have been rebooked to continue their journey on a later flight."
The passenger on the flight earlier told the Herald the passenger was escorted off the plane by security and engineering staff.
The pilot said "given the situation in Christchurch we are obviously taking no chances".
The pilot's earlier announcement had been met with audible shock and disapproval by other passengers.
One woman was heard to say, "Seriously? That is just unbelievable".
The security scare delayed the plane's take-off by 40 minutes.
There were also government employees on the delayed flight bound for Christchurch, including several officials from the department of internal affairs. They were travelling to attend tomorrow's memorial service for the victims of the Mosques massacre.
Aviation security has been stepped up following the March 15 mosque attacks.
In Christchurch, security screening has been put in place for domestic flights departing the city which have 30 passenger seats or more. Previously screening was just done on jet flights, such as the one subject to the scare in Auckland today.
The Aviation Security Service says it was a prudent risk management measure and could be rolled out at other airports.
''The appropriateness of current domestic security screening settings at airports other than Christchurch is the subject of ongoing review, as is always the case,'' said a spokesman.