Two Jetstar pilots have been stood down and an investigation launched into a flight to New Zealand earlier this month.
A spokesman for the airline today said "the wrong flap position" was selected as the flight from Sydney prepared to divert away from its destination of Christchurch on June 3.
The plane was involved in an aborted landing at Christchurch due to bad weather and instead landed in Auckland.
The flap position was "quickly fixed", the spokesman said.
"Jetstar understands the significance of this and is completing an assessment of exactly what happened and why," he said.
"Any suggestion that the fundamental safety of this aircraft or the people on it was at risk is simply untrue."
Jetstar has started an internal investigation and will pass on its findings to Australia's Civil Aviation Safety Authority (CASA).
It says it is normal practice for pilots to be stood down while it assesses an "in-flight event".
"We take anything that happens in the cockpit very seriously. We are assessing the issue and our initial findings show that the fundamental safety of the flight was never at risk," the airline spokesman said.
"Jetstar has well-trained pilots operating some of the most modern aircraft available. And we work in one of the most tightly regulated industries anywhere in the world, which is as it should be."
The Civil Aviation Authority (CAA) in New Zealand said it would not investigate because Jetstar safety was governed by Australian authorities.
The airline operates in New Zealand under "mutual recognition privileges".
"We will be provided with a report once that investigation (into the Jetstar flight landing) is completed by CASA, but any actions are between CASA and Jetstar," a spokeswoman for CAA said.
A spokesman for CASA said the authority would review Jetstar's report and "ensure that any appropriate safety actions are taken".