Pacific Blue admits one of its flights out of Queenstown took off four minutes after the shut-off point for departures in the evening.
The Civil Aviation Authority (CAA) is investigating the incident in which flight DJ 89 from Queenstown to Sydney on Tuesday, June 22, departed Queenstown Airport in darkness, potentially endangering the 140 passengers and crew aboard.
Pacific Blue said its internal procedure states aircraft at Queenstown should take off no later than 30 minutes before evening twilight.
It said on this occasion the plane took off about 26 minutes before twilight.
"After take-off the aircraft climbed at a safe and legal height in accordance with the weather conditions at the time and followed the prescribed visual departure procedure to continue its course to Sydney," Pacific Blue said in a statement.
Pacific Blue said it was co-operating with the Civil Aviation investigation and was also investigating the incident itself.
The airline said it began its investigation on June 24.
The airline also said the two senior pilots involved in the flight had been suspended from duty while investigations took place.
Queenstown Airport is surrounded by mountainous terrain and has no radar or runways lights.
CAA spokesman Bill Sommer today said airlines operating out of Queenstown must depart no later than 30 minutes before twilight as a safety precaution.
"If anything does happen, they've got sufficient time to return to the airfield and land," he said.
"The rules down there for the airlines are clear."
The Boeing 737 "appears to have taken off late" and investigators would speak to the pilot, the airline and witnesses.
"We're determining what happened and the circumstances around it," Sommer said.
Airlines operating out of Queenstown were responsible for enforcing the flight rules.
Witnesses said the Pacific Blue plane flew dangerously low to avoid low fog and an incoming front.
One witness said the plane was "banking almost on its side".
Queenstown harbour master Marty Black said the plane was "bloody low" and did not climb as it should have.
"It flew into a white-out ... the plane just disappeared.
"Obviously the heart started to race a little bit. I was concerned, I thought the plane was in trouble."
He complained to the CAA, along with three other concerned locals.
The CAA was now investigating three main areas of concern - that the plane took off in low light, bad weather and strong crosswinds.
CAA Director Steve Douglas said any case where rules are breached does cut into safety margins and that can ultimately put lives at risk.
He said because the alpine airport has no runway lights, and is nestled in mountainous terrain, the visual flight rules must be followed strictly.
Meanwhile, Prime Minister John Key said he had only heard media reports of the incident but that if they were true it was very concerning.
"New Zealand takes its record in terms of commercial aviation safety very seriously.
"My understanding is that Civil Aviation will be investigating the matter, and rightfully so."