"It is regrettable and we are working hard to resolve it."
Wind forecasting was important and Air New Zealand had been doing flight plans for over a year, modelling the route, Morgan told Hosking.
"The airline industry works on 80 percentile wind. Right now we are seeing 98 percentile of wind.
"We have to de risk ourselves to the operation being affected by those winds so we free the load of the passengers going southbound moving forward."
Morgan said on the first and the fourth flight the planes had to divert the flight route due to a cyclone.
"Particularly on the first flight, we were dealt a blow with a requirement to route around the cyclone that was heading from Florida that subsequently hit the Eastern seaboard of Canada, so that was something we had to avoid and the fourth flight there was a similar problem."
Hosking asked Morgan if the flight would then have a stop at Fiji, making it an indirect flight.
Morgan replied, "We need to make this route a direct flight to Auckland and it is our intention to operate what is the fourth longest flight in the world from JFK to AKL.
"A refuelling stop is always an option of course but that is what we only ever want to do in exceptional circumstances.
"It is disappointing that we had to think about it obviously in the first week, consequently we are working hard to not have to do that."
Talking to his colleagues in other airlines who do longer flights, Morgan said they had encountered similar issues starting out.
"They were doing their modelling based on historical data .. so we have had equal issues. Climate has changed now."
Morgan said Air New Zealand had ordered new aircraft from Boeing which were more optimal to the direct route.
"We are waiting for more aircraft to come from Boeing to make the flight normalised. At the moment we are flying aircraft which are not optimal.
"We need a better plane which has been ordered."
On Sunday, Air New Zealand passengers were asked to volunteer to miss an overweight flight from John F. Kennedy International Airport in New York due to strong headwinds on the return leg.
The airline called for 20 volunteers to miss the flight in exchange for US$1500 ($2591) and paid hotel accommodation, a passenger told the Herald.
An airline spokeswoman had said to compensate for the extra fuel required to fly into the headwind, and to avoid a stop in Fiji, the airline had to move 15 passengers on to alternative routes leaving today and tomorrow.
Earlier this week a flight on the new route was at one stage thought to need a stop in Fiji to refuel due to weather issues.
However, this was avoided after changes to the route while airborne, the spokeswoman said.
The inaugural 787 flight suffered similar issues with strong headwinds and difficult weather, leading the flight to offload passenger luggage and take on additional fuel in order to make the ultra-long route.
The airline - which launched the flagship route last weekend - began a review after that incident.
